Do plants need niches? Some recent developments in plant community ecology

Species-rich plant communities appear to defy the competitive exclusion principle, showing relatively few obvious niche differences between coexisting species. Here we explore alternatives to the potentially endless search for new niche axes. Spatial aggregation in populations, non-transitive competition, episodes of density-independent mortality and various non-equilibrium theories allow trophically similar species to coexist for extended periods. In perennial plants or annuals with a seed pool, asynchrony between species in recruitment permits coexistence by the 'storage effect'. There is increasing evidence that species-specific herbivores and pathogens regulate populations of tropical trees to low levels at which competitive exclusion does not occur. The wide variety of alternatives to niche differentiation lead us to question whether plants need occupy different niches to coexist.     

Species assortment or habitat filtering: a case study of spider communities on lake islands

Competition theory predicts that species of similar ecological niches are less likely to coexist than species with different niches, a process called species assortment. In contrast, the concept of habitat filtering implies that species with similar ecological requirements should co-occur more often than expected by chance. Here we use environmental and ecological data to assess patterns of co-occurrence of regional communities of spiders distributed across two assemblies of lake islands in northern Poland. We found aggregated and random co-occurrences of species of the same genus and a significant tendency of species segregation across genera. We also found that species of the same genus react similarly to important environmental variables. A comparison of ecological traits of species of the local communities with those expected from a random sample from the regional Polish species pool corroborated partly the habitat filtering hypothesis. On the other hand, we did not find evidence for species assortment. Our results also imply that at least some observed species co-occurrences result from niche differentiation.     

Plant and animal stem cells: conceptually similar, molecularly distinct?

Animals and plants maintain small pools of stem cells that continuously provide the precursors of more-specialized cells to sustain growth or to replace tissues. A comparison of plant and animal stem cells can highlight core aspects of stem-cell biology. In both types of organism, stem cells are maintained by intercellular signals that are available only in defined regions (niches) in the tissues. Although plants use different signals and are more flexible at establishing stem-cell niches in new locations, recent evidence suggests that the mechanisms restricting cell fate in stem-cell progeny are similar in both kingdoms and might pre-date the evolution of multicellular organisms.     

Two-patch model of spatial niche segregation

Spatial niche segregation between two habitats and the related adaptive dynamics are investigated. Independent population regulations operate in the two patches by a single resource in each. The populations migrate between the habitats with a constant rate. In line with a general mathematical concept published elsewhere, the niche of a species is described by the measures of the two-way interactions between the species and the resources. Increasing migration rate tends to equalize the population sizes between the habitats and diminish the dependence of the niches on the environmental tolerances of the species. In line with the expectations, when two species coexist, their realized niches are more segregated than their fundamental ones. We demonstrate that robust coexistence requires sufficient niche segregation. That is, the parameter range that allows coexistence of the two species shrinks to nil when the niche-differences between the species disappear. In turn, niche segregation requires separation of tolerances and sufficiently low migration rate. For the evolutionary study we assume a continuous, clonally inherited character that has different optima at the two patches. Evolution of this trait may end up in an intermediate “generalist” optimum, or it can branch and leads to a dimorphic population. The condition of the latter outcome is in line with the conditions that allow niche segregation: the patches have to be sufficiently different and the migration has to be sufficiently low. Electronic supplementary material  The online version of this article () contains supplementary material, which is available to authorized users.     

Geographical and ecological distributions of frog hemiclones suggest occurrence of both 'General-Purpose Genotype' and 'Frozen Niche Variation' clones

Asexuals often occupy broad geographical and ecological ranges. Two models have been proposed to explain the ubiquity of asexuals: the General‐Purpose Genotype (GPG) and the Frozen Niche Variation (FNV) model. According to these models, asexuals differ in their ecological niche width and may occupy narrow specialist niches or ubiquitous niches. A thousand water frogs from 37 different populations located in France in different habitats were studied, and two (hemi)clonal hybrid types were identified genetically, Rana esculenta and R. grafi. Altogether, 13 hemiclones were identified both in R. grafi and R. esculenta. Three of these were geographically and ecologically widely distributed, and usually very common in populations. In contrast, the remaining 10 hemiclones had small geographical ranges and were restricted to special habitat types, suggesting ecological niche specialization. The results suggest that in hybridogenetic water frogs GPG and FNV hemiclones coexist.     

Environmental Influence on the Evolution of Morphological Complexity in Machines

Whether, when, how, and why increased complexity evolves in biological populations is a longstanding open question. In this work we combine a recently developed method for evolving virtual organisms with an information-theoretic metric of morphological complexity in order to investigate how the complexity of morphologies, which are evolved for locomotion, varies across different environments. We first demonstrate that selection for locomotion results in the evolution of organisms with morphologies that increase in complexity over evolutionary time beyond what would be expected due to random chance. This provides evidence that the increase in complexity observed is a result of a driven rather than a passive trend. In subsequent experiments we demonstrate that morphologies having greater complexity evolve in complex environments, when compared to a simple environment when a cost of complexity is imposed. This suggests that in some niches, evolution may act to complexify the body plans of organisms while in other niches selection favors simpler body plans.     

Absence of phylogenetic signal in the niche structure of meadow plant communities

A significant proportion of the global diversity of flowering plants has evolved in recent geological time, probably through adaptive radiation into new niches. However, rapid evolution is at odds with recent research which has suggested that plant ecological traits, including the beta- (or habitat) niche, evolve only slowly. We have quantified traits that determine within-habitat alpha diversity (alpha niches) in two communities in which species segregate on hydrological gradients. Molecular phylogenetic analysis of these data shows practically no evidence of a correlation between the ecological and evolutionary distances separating species, indicating that hydrological alpha niches are evolutionarily labile. We propose that contrasting patterns of evolutionary conservatism for alpha- and beta-niches is a general phenomenon necessitated by the hierarchical filtering of species during community assembly. This determines that species must have similar beta niches in order to occupy the same habitat, but different alpha niches in order to coexist.     

Gene-flow between niches facilitates local adaptation in sexual populations

In sexual populations, gene-flow between niches is predicted to have differential consequences on local adaptation contingent upon the nature of trade-offs underlying local adaptation. Sex retards local adaptation if antagonistic pleiotropy underlies trade-offs, but facilitates adaptation if mutation accumulation underlies trade-offs. We evaluate the effect of sex in heterogeneous environments by manipulating gene-flow between two niches in sexual and asexual populations using steady-state microcosm experiments with yeast. We find that only sex in the presence of gene-flow promotes simultaneous local adaptation to different niches, presumably as this exposes mutations neutrally accrued in alternate niches to selection. This finding aligns with work showing mutation accumulation underlies trade-offs to local adaptation in asexual microbes, and with inferences of divergence in the presence of gene-flow in natural sexual populations. This experiment shows that sex may be of benefit in heterogeneous environments, and thus helps explain why sex has been maintained more generally.     

Do ecological niches differ between sexual and asexual lineages of an aphid species?

According to environmental-based theories on the maintenance of sexual reproduction, sexual and asexual populations may coexist if they occupy different ecological niches. The aphid Rhopalosiphum padi offers a good opportunity to test this hypothesis since sexual and asexual lineages show local coexistence during a large part of their respective life-cycles. Because these two reproductive variants are morphologically identical but genetically distinct, we first characterized them using genetic markers in populations of R. padi in areas where sexual and asexual lineages may occur in sympatry. We then inferred the natal host plant of sexual and asexual genotypes by analysing stable isotopic ratios and showed that sexual ones mostly originated from C₃ Poaceae while asexual ones originated from C₃ and C₄ plants, although the majority came from C₄ Poaceae. These findings indicate that ecological niches of sexual and asexual lineages of R. padi differ, offering a plausible explanation for the local coexistence of the two reproductive modes in this species through habitat specialisation.     

Competitive coexistence of self-reproducing macromolecules.

Several model systems of self-reproducing molecular species subject to the constraint of constant organization are investigated to see under what conditions more than one species may coexist over extended periods of time. It is found that while coexistence is not possible for systems of simple autocatalytic competitors, it can indeed occur if the nature of the reproductive process gives rise to “catalytic niches”. For systems catalyzed by n Michaelis-Menten type enzymes, it is shown that no more than n species may coexist. A precise characterization is provided of “how different” two such enzymes must be in order to allow coexistence of two species. Under certain conditions, one observes a transition from one dominant species to another which may occur either via a coexistent state or directly, but with hysteresis.     

Imitating the cost of males: A hypothesis for coexistence of all‐female sperm‐dependent species and their sexual host

All‐female sperm‐dependent species are particular asexual organisms that must coexist with a closely related sexual host for reproduction. However, demographic advantages of asexual over sexual species that have to produce male individuals could lead both to extinction. The unresolved question of their coexistence still challenges and fascinates evolutionary biologists. As an alternative hypothesis, we propose those asexual organisms are afflicted by a demographic cost analogous to the production of males to prevent exclusion of the host. Previously proposed hypotheses stated that asexual individuals relied on a lower fecundity than sexual females to cope with demographic advantage. In contrast, we propose that both sexual and asexual species display the same number of offspring, but half of asexual individuals imitate the cost of sex by occupying ecological niches but producing no offspring. Simulations of population growth in closed systems under different demographic scenarios revealed that only the presence of nonreproductive individuals in asexual females can result in long‐term coexistence. This hypothesis is supported by the fact that half of the females in some sperm‐dependent organisms did not reproduce clonally.     

How generalists coexist: the role of floral phenotype and spatial factors in the pollination systems of two Ranunculus species

Aims Competition for pollinators between phenotypically similar flowers is believed to play an important role in floral trait diversification in the angiosperms. However, in many plant communities, species with apparently similar floral phenotypes and generalist pollination systems co-flower. Here, the pollination systems of Ranunculus acris L. and Ranunculus repens L. were investigated to determine the factors enabling the species to coexist within apparently overlapping pollination niches.Methods Sympatrically flowering populations of R. acris and R. repens were investigated at three study sites in West Wales. The floral phenotypes of the two species were compared using measurements of floral morphology and spectral analyses of petal reflectance, using principal component analysis and bee and fly colour-space models. Evidence of inter-specific discrimination by foraging insects was tested for in the field and using floral arrays. The relative roles of behavioural constancy and spatial patchiness in maintaining pollinator fidelity were estimated.Important findings The floral phenotypes of R. acris and R. repens differed significantly. Social bees were highly constant when foraging at flowers of the two species and patchy floral distribution explained some of the observed fidelity. Dipterans visiting mixed floral arrays appeared to discriminate between the species, visiting more R. acris than R. repens flowers, but there was no difference in the number of visits to single-species arrays. Social bees were more likely to display constancy to flowers of R. repens in the field. Patchiness in floral distribution, subtle differences in floral phenotype, pollinator preferences and behavioural constancy are all likely to contribute to the continued coexistence of R. acris and R. repens, despite apparent overlap in their pollination niches. Such differences have the potential to facilitate the maintenance of species diversity in plant communities, even where plants appear to share similar floral phenotypes.     

GENETIC CORRELATIONS BETWEEN LIFE-HISTORY AND BEHAVIORAL TRAITS CAN CAUSE REPRODUCTIVE ISOLATION

Reproductive isolation may often evolve as an indirect (pleiotropic) consequence of populations adapting to different environments or habitats. For example, niches that are temporally or seasonally offset can select for organisms with different developmental characteristics. These developmental differences can inadvertently cause reproductive isolation by a variety of means including shifts in mating activity patterns. Here, we show a genetic correlation between a life-history trait (developmental period) and a behavioral trait (time of mating) that causes significant premating isolation in the melon fly, Bactrocera cucurbitae (Diptera: Tephritidae). Fly lines selected for short and long developmental periods differ in their preferred times of mating during the evening. This difference translates into significant prezygotic isolation, as measured by mate choice tests. If the time of mating between two populations differed more than one hour, the isolation index was significantly higher than zero. These indicate that premating isolation can be established if the developmental period is divergently selected for. If such genetic correlations are ubiquitous in many organisms, multifarious divergent selection for life-history traits would often accelerate the evolution of reproductive isolation. We speculate that reproductive isolation may have been evolved via genetic correlations among time-related traits, for example, developmental period and time of mating, as in other organisms.     

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.     

Ecological distribution and niche segregation of sibling species: the case of bean beetles, Acanthoscelides obtectus Say and A. obvelatus Bridwell

Abstract.  1. Molecular techniques have greatly added to the number of known sympatric cryptic species in insects. Ecological differences between these newly distinguished species are little explored, but niches often appear to overlap strongly. These cases are good models for exploring new ideas about species coexistence and community structure.
2.  Acanthoscelides obtectus and A. obvelatus are two sister species of bean bruchids, which have been confused until the last decade. One important ecological difference between them has emerged, however: A. obtectus is multivoltine and now distributed worldwide, whereas A. obvelatus is univoltine and restricted to Mesoamerica. Where their ranges overlap, the two species share the same host plants and larvae can sometimes complete development in the same seed.
3. The analysis of 27 622 Mexican individuals of the two species in 2001-2002 and 2002-2003 indicates that their niches overlap, but are differentiated with respect to altitude and the kind of beans (wild vs. domesticated). The principal patterns in their relative abundance in different habitats, and at different seasons, were constant from one year to the next.
4. As sympatry of these species seems to be of recent origin, the observed niche differentiation may not have evolved in response to competition, but could instead be the consequence of physiological differences, evolved independently in each species in allopatry, that pre-adapted them for different altitudes and kinds of resources.
5. The combination of biological and historical factors thus appears to allow these two sibling species to coexist in sympatry, despite their broadly overlapping ecological niches.     

Diversity of free-living ‘naked’ amoeboid organisms

Amoeboid organisms are phylogenetically diverse, some being more closely related to plants or metazoans than to each other. Amoeboid organisms are ecologically successful, having been isolated on all continents, including Antarctica, as well as being the main predators controlling bacterial populations in soil. The classification of these organisms has historically relied upon morphological characteristics. The application of electron microscopy, comparison of enzymic profiles after electrophoretic separation, and analysis of nucleic acid fractions have provided reliable bases for classifying amoeboid organisms. The extent of diversity of these organisms has been recognized, as methods to detect, culture, characterize and identify them has increased. It is reasonable to anticipate that the current 40 000 species of protists will increase substantially as amoeboid organisms are cultivated from poorly accessible niches and from extreme environs.     

Phylogenetic niche conservatism and the evolutionary basis of ecological speciation

Phylogenetic niche conservatism (PNC) typically refers to the tendency of closely related species to be more similar to each other in terms of niche than they are to more distant relatives. This has been implicated as a potential driving force in speciation and other species‐richness patterns, such as latitudinal gradients. However, PNC has not been very well defined in most previous studies. Is it a pattern or a process? What are the underlying endogenous (e.g. genetic) and exogenous (e.g. ecological) factors that cause niches to be conserved? What degree of similarity is necessary to qualify as PNC? Is it possible for the evolutionary processes causing niches to be conserved to also result in niche divergence in different habitats? Here, we revisit these questions, codifying a theoretical and operational definition of PNC as a mechanistic evolutionary process resulting from several factors. We frame this both from a macroevolutionary and population‐genetic perspective. We discuss how different axes of physical (e.g. geographic) and environmental (e.g. climatic) heterogeneity interact with the fundamental process of PNC to produce different outcomes of ecological speciation. We also review tests for PNC, and suggest ways that these could be improved or better utilized in future studies. Ultimately, PNC as a process has a well‐defined mechanistic basis in organisms, and future studies investigating ecological speciation would be well served to consider this, and frame hypothesis testing in terms of the processes and expected patterns described herein. The process of PNC may lead to patterns where niches are conserved (more similar than expected), constrained (divergent within a limited subset of available niches), or divergent (less similar than expected), based on degree of phylogenetic relatedness between species.     

Death and cannibalism in a seasonal environment facilitate bacterial coexistence

Bacterial populations can evolve and adapt to become diverse niche specialists, even in seemingly homogeneous environments. One source of this diversity arises from newly 'constructed' niches that result from the activities of the bacteria themselves. Ecotypes specialized to exploit these distinct niches can subsequently coexist via frequency-dependent interactions. Here, we describe a novel form of niche construction that is based upon differential death and cannibalism, and which evolved during 20 000 generations of experimental evolution in Escherichia coli in a seasonal environment with alternating growth and starvation. In one of 12 populations, two monophyletic ecotypes, S and L, evolved that stably coexist with one another. When grown and then starved in monoculture, the death rate of S exceeds that of L, whereas the reverse is observed in mixed cultures. As shown by experiments and numerical simulations, the competitive advantage of S cells is increased by extending the period of starvation, and this advantage results from their cannibalization of the debris of lysed L cells, which allows the S cells to increase both their growth rate and total cell density. At the molecular level, the polymorphism is associated with divergence in the activity of the alternative sigma factor RpoS, with S cells displaying no detectable activity, while L cells show increased activity relative to the ancestral genotype. Our results extend the repertoire of known cross-feeding mechanisms in microbes to include cannibalism during starvation, and confirm the central roles for niche construction and seasonality in the maintenance of microbial polymorphisms.     

The timescale of environmental fluctuations determines the competitive advantages of phenotypic plasticity and rapid evolution

Organisms can respond to fluctuating environments by phenotypic plasticity and rapid evolution, both occurring on similar timescales to the environmental fluctuations. Because each adaptation mechanism has been independently studied, the effects of different adaptation mechanisms on ecological dynamics are not well understood. Here, using mathematical modeling, we compared the advantages of phenotypic plasticity and rapid evolution under conditions where the environment fluctuated between two states on various timescales. The results indicate that the advantages of phenotypic plasticity under environmental fluctuations on different timescales depend on the cost and the speed of plasticity. Both the speed of plastic adaptation and the cost of plasticity affect competition results, while the quantitative effects of them vary depending on the timescales. When the environment fluctuates on short timescales, the two populations with evolution and plasticity coexist, although the population with evolution is dominant. On moderate timescales, the two populations also coexist; however, the population with plasticity becomes dominant. On long timescales, whether the population with phenotypic plasticity or evolution is more advantageous depended on the cost of plasticity. Moreover, our results indicate that the mechanisms resulting in the dominance of the plastic population over the population with evolution are different depending on the timescales of environmental fluctuations. Therefore, the timescales of environmental fluctuations deserve more attention if we are to better understand the detailed competition results underlying phenotypic variation.     

Modeling microbial dynamics in heterogeneous environments: growth on soil carbon sources

We have developed a new kinetic model to study how microbial dynamics are affected by the heterogeneity in the physical structure of the environment and by different strategies for hydrolysis of polymeric carbon. The hybrid model represented the dynamics of substrates and enzymes using a continuum representation and the dynamics of the cells were modeled individually. Individual-based biological model allowed us to explicitly simulate microbial diversity, and to model cell physiology as regulated via optimal allocation of cellular resources to enzyme synthesis, control of growth rate by protein synthesis capacity, and shifts to dormancy. This model was developed to study how microbial community functioning is influenced by local environmental conditions in heterogeneous media such as soil and by the functional attributes of individual microbes. Microbial community dynamics were simulated at two spatial scales: micro-pores that resemble 6-20-μm size portions of the soil physical structure and in 111-μm size soil aggregates with a random pore structure. Different strategies for acquisition of carbon from polymeric cellulose were investigated. Bacteria that express membrane-associated hydrolase had different growth and survival dynamics in soil pores than bacteria that release extracellular hydrolases. The kinetic differences suggested different functional niches for these two microbe types in cellulose utilization. Our model predicted an emergent behavior in which co-existence of membrane-associated hydrolase and extracellular hydrolases releasing organisms led to higher cellulose utilization efficiency and reduced stochasticity. Our analysis indicated that their co-existence mutually benefits these organisms, where basal cellulose degradation activity by membrane-associated hydrolase-expressing cells shortened the soluble hydrolase buildup time and, when enzyme buildup allowed for cellulose degradation to be fast enough to sustain exponential growth, all the organisms in the community shared the soluble carbon product and grew together. Although pore geometry affected the kinetics of cellulose degradation, the patterns observed for the bacterial community dynamics in the 6-20 μm-sized micro-pores were relevant to the dynamics in the more complex 111-μm-sized porous soil aggregates, implying that micro-scale studies can be useful approximations to aggregate scale studies when local effects on microbial dynamics are studied. As shown with examples in this study, various functional niches of the bacterial communities can be investigated using complex predictive mathematical models where the role of key environmental aspects such as the heterogeneous three-dimensional structure, functional niches of the community members, and environmental biochemical processes are directly connected to microbial metabolism and maintenance in an integrated model.