From antagonistic larvae to mutualistic adults: coevolution of diet niches within life cycles

Population structures largely affect higher levels of organization (community structure, ecosystem functioning), especially when involving ontogenetic changes in habitat or diet. Along life cycles, partners and interaction type may change: for instance Lepidopterans are herbivores as larvae and pollinators as adults. To understand variations in diet niche from larvae to adults, we model a community of two plant species and one stage‐structured insect species consuming plants as juvenile and pollinating them as adult. We model the coevolution of juvenile and adult diet specialization using adaptive dynamics to investigate when one should expect niche partitioning or niche overlap among life stages. We consider ecological and evolutionary implications for the coexistence of species. As predicted based on indirect effects among stages, we find that juvenile diet evolution increases niche overlap and favours the coexistence of plants, while the evolution of the adult diet decreases niche overlap and reduces plant coexistence, because of positive feedbacks emerging from the mutualistic interaction.     

Complex life cycles in a pond food web: effects of life stage structure and parasites on network properties,trophic positions and the fit of a probabilistic niche model

Most food webs use taxonomic or trophic species as building blocks, thereby collapsing variability in feeding linkages that occurs during the growth and development of individuals. This issue is particularly relevant to integrating parasites into food webs because parasites often undergo extreme ontogenetic niche shifts. Here, we used three versions of a freshwater pond food web with varying levels of node resolution (from taxonomic species to life stages) to examine how complex life cycles and parasites alter web properties, the perceived trophic position of organisms, and the fit of a probabilistic niche model. Consistent with prior studies, parasites increased most measures of web complexity in the taxonomic species web; however, when nodes were disaggregated into life stages, the effects of parasites on several network properties (e.g., connectance and nestedness) were reversed, due in part to the lower trophic generality of parasite life stages relative to free-living life stages. Disaggregation also reduced the trophic level of organisms with either complex or direct life cycles and was particularly useful when including predation on parasites, which can inflate trophic positions when life stages are collapsed. Contrary to predictions, disaggregation decreased network intervality and did not enhance the fit of a probabilistic niche model to the food webs with parasites. Although the most useful level of biological organization in food webs will vary with the questions of interest, our results suggest that disaggregating species-level nodes may refine our perception of how parasites and other complex life cycle organisms influence ecological networks.     

Evolution restricts the coexistence of specialists and generalists: the role of trade-off structure

Environmental variability and adaptive foraging behavior have been shown to favor coexistence of specialists and generalists on an ecological timescale. This leaves unaddressed the question of whether such coexistence can also be expected on an evolutionary timescale. In this article, we study the attainability, through gradual evolution, of specialist-generalist coexistence, as well as the evolutionary stability of such communities when allowing for immigration. Our analysis shows that the potential for specialist-generalist coexistence is much more restricted than originally thought and strongly depends on the trade-off structure assumed. We establish that ecological coexistence is less likely for species facing a trade-off between per capita reproduction in different habitats than when the trade-off acts on carrying capacities alone. We also demonstrate that coexistence is evolutionarily stable whenever it is ecologically stable but that in most cases, such coexistence cannot be reached through gradual evolution. We conclude that an evolutionarily stable community of specialists and generalists may be created only through immigration from elsewhere or through mutations of large effect. Our results highlight that trade-offs in fitness-determining traits can have counterintuitive effects on the evolution of specialization.     

High-dimensional coexistence of temperate tree species: functional traits, demographic rates, life-history stages, and their physical context

Theoretical models indicate that trade-offs between growth and survival strategies of tree species can lead to coexistence across life history stages (ontogeny) and physical conditions experienced by individuals. There exist predicted physiological mechanisms regulating these trade-offs, such as an investment in leaf characters that may increase survival in stressful environments at the expense of investment in bole or root growth. Confirming these mechanisms, however, requires that potential environmental, ontogenetic, and trait influences are analyzed together. Here, we infer growth and mortality of tree species given size, site, and light characteristics from forest inventory data from Wisconsin to test hypotheses about growth-survival trade-offs given species functional trait values under different ontogenetic and environmental states. A series of regression analyses including traits and rates their interactions with environmental and ontogenetic stages supported the relationships between traits and vital rates expected from the expectations from tree physiology. A combined model including interactions between all variables indicated that relationships between demographic rates and functional traits supports growth-survival trade-offs and their differences across species in high-dimensional niche space. The combined model explained 65% of the variation in tree growth and supports a concept of community coexistence similar to Hutchinson's n-dimensional hypervolume and not a low-dimensional niche model or neutral model.     

Reconciling niche and neutrality: the continuum hypothesis

In this study, we ask if instead of being fundamentally opposed, niche and neutral theories could simply be located at the extremes of a continuum. First, we present a model of recruitment probabilities that combines both niche and neutral processes. From this model, we predict and test whether the relative importance of niche vs. neutral processes in controlling community dynamics will vary depending on community species richness, niche overlap and dispersal capabilities of species (both local and long distance). Results demonstrate that niche and neutrality form ends of a continuum from competitive to stochastic exclusion. In the absence of immigration, competitive exclusion tends to create a regular spacing of niches. However, immigration prevents the establishment of a limiting similarity. The equilibrium community consists of a set of complementary and redundant species, with their abundance determined, respectively, by the distribution of environmental conditions and the amount of immigration.     

Ontogenetic niche shifts matter in community ecology: a review and future perspectives

Almost all organisms on Earth exhibit ontogenetic niche shifts, which causes great phenotypic variation among individuals and is thus considered to critically mediate community structure and dynamics. In contrast, community ecology has traditionally assumed that species are composed of identical individuals with invariant traits and ignored the potentially important ecological roles of ontogenetic niche shifts. To bridge the gap, here I briefly review ecologically relevant examples which show that basic insights of species-based community theories can be revised by including the ontogenetic perspective. Specifically, I focus on the most representative animals in the study of ontogenetic niche shifts, i.e., fish, insects, and amphibians. Notably, their ontogenetic niche shifts create novel views of community structure: (1) ontogenetic diet shifts of predatory fish couple pelagic and benthic food webs in aquatic systems, (2) ontogenetic shifts in interaction types of pollinating insects couple herbivory and pollination networks in terrestrial systems, and (3) ontogenetic habitat shifts of amphibians and aquatic insects couple aquatic and terrestrial metacommunities at interface areas. Dynamic models of such stage-structured communities suggest that their ontogenetic niche shifts may affect the community resilience and disturbance responses. Exploring more complex systems (e.g., where many species undergo ontogenetic niche shifts several times or continuously) is a future direction, for which describing body size relationships between interacting organisms would be a promising approach. I conclude that both theoretical and empirical advances are needed to facilitate the ontogenetic perspective for better understanding mechanisms underlying biodiversity and ecosystem functioning which are increasingly threatened by anthropogenic disturbance.     

Reduced vegetation integrity in selectively logged Atlantic rainforest affects bird diversity: Higher taxonomic and functional diversity,but increased niche overlap

Although selectively logged tropical forests have high bird species richness, it is known that their species composition is substantially changed when compared with intact forests. Thus, we need to improve the understanding on how functional trait diversity of birds is affected in this habitat type in order to support the development of more effective conservation actions to maintain functional roles and community stability. Here, we evaluate traits responses to variations in forest vegetation integrity and how the pattern of niche occupancy is affected by this increase in species richness. We then evaluated the effects of vegetation integrity in the Atlantic rainforest on range of trait space occupied, niche packing, and trait composition in local bird communities. We also evaluate the mechanisms driving niche expansion and packing using null models. Our results show that trait composition changes in communities: (1) lower vegetation integrity increases foraging in understory and consumption of grains and ectothermic vertebrates by birds; (2) higher vegetation integrity drives higher and wider beaks and increase foraging for invertebrates in canopy. We also found that lower vegetation integrity not only is associated with the increase of species richness, but also with both expansion and packing of niche space occupied by the community. However, only niche packing had predominantly smaller values than expected by chance, indicating a strong effect of environmental filters on niche occupancy density. Although bird assemblages in more intact vegetations have lower species richness, they have greater functional distance between bird species suggesting greater stability, with a low probability of local extinctions due to a lower intensity of interspecific competition. This demonstrates that isolated assessments of species richness are potentially illusory and can lead to unsuccessful conservation measures, such as proposing selective logging in primary forests based on the supposed benefit of increased bird species richness in vegetations less intact. Furthermore, the functional composition tends to change with changes in vegetation integrity degree, thus altering the functional role provided by communities. Consequently, forests with high vegetation integrity status should be maintained, despite the lower species richness.     

Strong species‐environment feedback shapes plant community assembly along environmental gradients

An aim of community ecology is to understand the patterns of competing species assembly along environmental gradients. All species interact with their environments. However, theories of community assembly have seldom taken into account the effects of species that are able to engineer the environment. In this modeling study, we integrate the species' engineering trait together with processes of immigration and local dispersal into a theory of community assembly. We quantify the species' engineering trait as the degree to which it can move the local environment away from its baseline state towards the optimum state of the species (species‐environment feedback). We find that, in the presence of immigration from a regional pool, strong feedback can increase local species richness; however, in the absence of continual immigration, species richness is a declining function of the strength of species‐environment feedback. This shift from a negative effect of engineering strength on species richness to a positive effect, as immigration rate increases, is clearer when there is spatial heterogeneity in the form of a gradient in environmental conditions than when the environment is homogeneous or it is randomly heterogeneous. Increasing the scale over which local dispersal occurs can facilitate species richness when there is no species‐environment feedback or when the feedback is weak. However, increases in the spatial scale of dispersal can reduce species richness when the species‐environment feedback is strong. These results expand the theoretical basis for understanding the effects of the strength of species‐environment feedback on community assembly.     

Developmental life history is associated with variation in rates of climatic niche evolution in a salamander adaptive radiation*

Rates of climatic niche evolution vary widely across the tree of life and are strongly associated with rates of diversification among clades. However, why the climatic niche evolves more rapidly in some clades than others remains unclear. Variation in life history traits often plays a key role in determining the environmental conditions under which species can survive, and therefore, could impact the rate at which lineages can expand in available climatic niche space. Here, we explore the relationships among life-history variation, climatic niche breadth, and rates of climatic niche evolution. We reconstruct a phylogeny for the genus Desmognathus, an adaptive radiation of salamanders distributed across eastern North America, based on nuclear and mitochondrial genes. Using this phylogeny, we estimate rates of climatic niche evolution for species with long, short, and no aquatic larval stage. Rates of climatic niche evolution are unrelated to the mean climatic niche breadth of species with different life histories. Instead, we find that the evolution of a short larval period promotes greater exploration of climatic space, leading to increased rates of climatic niche evolution across species having this trait. We propose that morphological and physiological differences associated with variation in larval stage length underlie the heterogeneous ability of lineages to explore climatic niche space. Rapid rates of climatic niche evolution among species with short larval periods were an important dimension of the clade's adaptive radiation and likely contributed to the rapid rate of lineage accumulation following the evolution of an aquatic life history in this clade. Our results show how variation in a key life-history trait can constrain or promote divergence of the climatic niche, leading to variation in rates of climatic niche evolution among species.     

Emergence of complexity in evolving niche-model food webs

We have analysed mechanisms that promote the emergence of complex structures in evolving model food webs. The niche model is used to determine predator-prey relationships. Complexity is measured by species richness as well as trophic level structure and link density. Adaptive dynamics that allow predators to concentrate on the prey species they are best adapted to lead to a strong increase in species number but have only a small effect on the number and relative occupancy of trophic levels. The density of active links also remains small but a high number of potential links allows the network to adjust to changes in the species composition (emergence and extinction of species). Incorporating effects of body size on individual metabolism leads to a more complex trophic level structure: both the maximum and the average trophic level increase. So does the density of active links. Taking body size effects into consideration does not have a measurable influence on species richness. If species are allowed to adjust their foraging behaviour, the complexity of the evolving networks can also be influenced by the size of the external resources. The larger the resources, the larger and more complex is the food web it can sustain. Body size effects and increasing resources do not change size and the simple structure of the evolving networks if adaptive foraging is prohibited. This leads to the conclusion that in the framework of the niche model adaptive foraging is a necessary but not sufficient condition for the emergence of complex networks. It is found that despite the stabilising effect of foraging adaptation the system displays elements of self-organised critical behaviour.     

Ecomorphological analysis of fish taxocenes in rainforest streams of northern Borneo

Average species richness for fish taxocenes in the Nida River (Poland), Grand River (Ontario) and Baram River (Sarawak, Malaysia) was 7, 16 and 24 species respectively. Discriminant analysis of 15 morphological attributes indicated Baram fishes partitioned the habitat vertically into mainly surface, pelagic, benthic and substratum niche types. Attribute comparisons among the river systems revealed a progression towards more sedentary benthic morphologies with increasing average species richness. Similarly, niche compression as a consequence of increasing average species richness was indicated by a reduction in length of life and average size, and was associated with development of complex life-history and reproductive styles. Total niche space occupied by the fish taxocenes was comparable in the three river systems despite differences in species richness. The amount of species packing and niche space occupied by Baram fish taxocenes were also not related to the numbers of species present. Fish community structure was apparently determined by the range of available resources and the associated specializations of the coexisting species.     

Shape and size variation: Growth and development of the dusky grouper (Epinephelus marginatus Lowe, 1834)

Demersal fishes have complex life cycles that involve an ontogenetic change in morphology, physiology, and behavior, as their pelagic larval stages colonize benthic habitats. The developmental transition between larvae and juveniles leads to very complex processes of morphogenesis and differentiation. These processes primarily determine changes in external morphology, which is shaped by selective pressures to optimize performance for basic activities such as swimming, escape from predators, and feeding. Fishes have provided fertile grounds for ecomorphological investigations throughout ontogeny, as the role of changing morphology in inducing ontogenetic niche shifts is not always clear. In this framework, some studies have demonstrated that certain species undergo gradual changes, whereas other species experience threshold effects in their ecomorphological relationships during ontogeny. In this study, the intraspecific allometry of the dusky grouper was examined. Geometric morphometric tools were used to quantify shape changes through the development, and a modular approach was also applied to analyze the pattern of covariation between three distinct blocks (head, trunk, and tail). For this purpose, a two‐block Partial Least Square was computed. This method reveals that the pattern of changes in the overall body shape is the result of the modularized changes of these blocks. J. Morphol., 2009. © 2008 Wiley‐Liss, Inc.     

Phylogenetic analysis of ecomorphological divergence, community structure, and diversification rates in dusky salamanders (Plethodontidae: Desmognathus)

An important dimension of adaptive radiation is the degree to which diversification rates fluctuate or remain constant through time. Focusing on plethodontid salamanders of the genus Desmognathus, we present a novel synthetic analysis of phylogeographic history, rates of ecomorphological evolution and species accumulation, and community assembly in an adaptive radiation. Dusky salamanders are highly variable in life history, body size, and ecology, with many endemic lineages in the southern Appalachian Highlands of eastern North America. Our results show that life-history evolution had important consequences for the buildup of plethodontid-salamander species richness and phenotypic disparity in eastern North America, a global hot spot of salamander biodiversity. The origin of Desmognathus species with aquatic larvae was followed by a high rate of lineage accumulation, which then gradually decreased toward the present time. The peak period of lineage accumulation in the group coincides with evolutionary partitioning of lineages with aquatic larvae into seepage, stream-edge, and stream microhabitats. Phylogenetic simulations demonstrate a strong correlation between morphology and microhabitat ecology independent of phylogenetic effects and suggest that ecomorphological changes are concentrated early in the radiation of Desmognathus. Deep phylogeographic fragmentation within many codistributed ecomorph clades suggests long-term persistence of ecomorphological features and stability of endemic lineages and communities through multiple climatic cycles. Phylogenetic analyses of community structure show that ecomorphological divergence promotes the coexistence of lineages and that repeated, independent evolution of microhabitat-associated ecomorphs has a limited role in the evolutionary assembly of Desmognathus communities. Comparing and contrasting our results to other adaptive radiations having different biogeographic histories, our results suggest that rates of diversification during adaptive radiation are intimately linked to the degree to which community structure persists over evolutionary time.     

Thirty Years of Forest Census at Barro Colorado and the Importance of Immigration in Maintaining Diversity

The neutral theory of community ecology can predict diversity and abundances of tropical trees, but only under the assumption of steady input of new species into the community. Without input, diversity of a neutral community collapses, so the theory''s predictions are not relevant unless novel species evolve or immigrate. We derive analytically the species input needed to maintain a target tree diversity, and find that a rate close to per recruit would maintain the observed diversity of 291 species in the Barro Colorado 50-ha tree plot in Panama. We then measured the rate empirically by comparing species present in one complete enumeration of the plot to those present five years later. Over six census intervals, the observed rate of input was to species per recruit, suggesting that there is adequate immigration of novel species to maintain diversity. Species interactions, niche partitioning, or density-dependence, while they may be present, do not appear to enhance tree species richness at Barro Colorado.     

What explains patterns of species richness? The relative importance of climatic‐niche evolution,morphological evolution,and ecological limits in salamanders

A major goal of evolutionary biology and ecology is to understand why species richness varies among clades. Previous studies have suggested that variation in richness among clades might be related to variation in rates of morphological evolution among clades (e.g., body size and shape). Other studies have suggested that richness patterns might be related to variation in rates of climatic‐niche evolution. However, few studies, if any, have tested the relative importance of these variables in explaining patterns of richness among clades. Here, we test their relative importance among major clades of Plethodontidae, the most species‐rich family of salamanders. Earlier studies have suggested that climatic‐niche evolution explains patterns of diversification among plethodontid clades, whereas rates of morphological evolution do not. A subsequent study stated that rates of morphological evolution instead explained patterns of species richness among plethodontid clades (along with “ecological limits” on richness of clades, leading to saturation of clades with species, given limited resources). However, they did not consider climatic‐niche evolution. Using phylogenetic multiple regression, we show that rates of climatic‐niche evolution explain most variation in richness among plethodontid clades, whereas rates of morphological evolution do not. We find little evidence that ecological limits explain patterns of richness among plethodontid clades. We also test whether rates of morphological and climatic‐niche evolution are correlated, and find that they are not. Overall, our results help explain richness patterns in a major amphibian group and provide possibly the first test of the relative importance of climatic niches and morphological evolution in explaining diversity patterns.     

Immigration,Local Dispersal Limitation,and the Repeatability of Community Composition under Neutral and Niche Dynamics

Repeatability of community composition has been a critical aspect for community structure, which is closely associated with community stability, predictability, conservation biology and ecological restoration. It has been shown that both immigration and local dispersal limitation can affect the community composition in both neutral and niche model. Hence, we use a spatially explicit individual-based model to investigate the potential influence of immigration rate and strength of local dispersal limitation on repeatability in both neutral and niche models. Similarity measures are used to quantify repeatability. We examine the repeatability of community composition among replicate communities (which means the same community repeats many times), and between niche and neutral replicate communities. We find the correlation between repeatability and immigration rate is positive in the neutral model and an inverted unimodal in the niche model. The correlation between repeatability and local dispersal distance is positive in the niche model and negative in the neutral model. High repeatability between niche communities and neutral communities is observed with high immigration rates or when high local dispersal distance appears in the niche model or low local dispersal distance in the neutral model. Our results show that repeatability of community composition is not only dependent on the types of community models (niche vs. neutrality) but also strongly determined by immigration rates and local dispersal limitation.     

Allee effects, immigration, and the evolution of species' niches

Theoretical studies of adaptation to sink environments (with conditions outside the niche requirements of a species) have shown that immigration from source habitats can either facilitate or inhibit local adaptation. Here, we examine the influence of immigration on the evolution of local adaptation, given an Allee effect (i.e., at low densities, absolute fitness increases with population density). We consider a deterministic model for evolution at a haploid locus, and a stochastic individual-based model for evolution of a quantitative trait, and several kinds of Allee effects. We demonstrate that increased immigration can greatly facilitate adaptive evolution in the sink; with greater immigration, local population sizes rise, and because of the Allee effect, there is a positive indirect effect of immigration on local fitness. This makes it easier for alleles of modest effect to be captured by natural selection, transforming the sink into a locally adapted population that can persist without immigration.     

Evolution of climatic niche specialization: a phylogenetic analysis in amphibians

The evolution of climatic niche specialization has important implications for many topics in ecology, evolution and conservation. The climatic niche reflects the set of temperature and precipitation conditions where a species can occur. Thus, specialization to a limited set of climatic conditions can be important for understanding patterns of biogeography, species richness, community structure, allopatric speciation, spread of invasive species and responses to climate change. Nevertheless, the factors that determine climatic niche width (level of specialization) remain poorly explored. Here, we test whether species that occur in more extreme climates are more highly specialized for those conditions, and whether there are trade-offs between niche widths on different climatic niche axes (e.g. do species that tolerate a broad range of temperatures tolerate only a limited range of precipitation regimes?). We test these hypotheses in amphibians, using phylogenetic comparative methods and global-scale datasets, including 2712 species with both climatic and phylogenetic data. Our results do not support either hypothesis. Rather than finding narrower niches in more extreme environments, niches tend to be narrower on one end of a climatic gradient but wider on the other. We also find that temperature and precipitation niche breadths are positively related, rather than showing trade-offs. Finally, our results suggest that most amphibian species occur in relatively warm and dry environments and have relatively narrow climatic niche widths on both of these axes. Thus, they may be especially imperilled by anthropogenic climate change.     

On the evolutionary stability of sink populations

The evolution of adaptive behaviours can influence population dynamics. Conversely, population dynamics can affect both the rate and direction of adaptive evolution. This paper examines reasons why sink populations – populations maintained by immigration, preventing local extinction – might persist in the habitat repertoire of a species over evolutionary time-scales. Two such reasons correspond to standard explanations for deviations from an ideal free habitat distribution: organisms may not be free to settle in whichever habitat has the highest potential fitness, and may be constrained by costs, perceptual limitations, or mode of dispersal in the acuity of their habitat selectivity. Here, I argue that a third general reason for persistent sink populations is provided by unstable population dynamics in source habitats. I present a simple model illustrating how use of a sink habitat may be selectively advantageous, when a source population has unstable dynamics (which necessarily reflects temporal variation in local fitnesses). Species with unstable local dynamics in high-quality habitats should be selected to utilize a broader range of habitats than species with stable local dynamics, and in particular in some circumstances should utilize sink habitats. This observation has implications for the direction of niche evolution, and the likelihood of niche conservatism.     

A stochastic, evolutionary model for range shifts and richness on tropical elevational gradients under Quaternary glacial cycles

Quaternary glacial-interglacial cycles repeatedly forced thermal zones up and down the slopes of mountains, at all latitudes. Although no one doubts that these temperature cycles have left their signature on contemporary patterns of geography and phylogeny, the relative roles of ecology and evolution are not well understood, especially for the tropics. To explore key mechanisms and their interactions in the context of chance events, we constructed a geographical range-based, stochastic simulation model that incorporates speciation, anagenetic evolution, niche conservatism, range shifts and extinctions under late Quaternary temperature cycles along tropical elevational gradients. In the model, elevational patterns of species richness arise from the differential survival of founder lineages, consolidated by speciation and the inheritance of thermal niche characteristics. The model yields a surprisingly rich variety of realistic patterns of phylogeny and biogeography, including close matches to a variety of contemporary elevational richness profiles from an elevational transect in Costa Rica. Mountaintop extinctions during interglacials and lowland extinctions at glacial maxima favour mid-elevation lineages, especially under the constraints of niche conservatism. Asymmetry in temperature (greater duration of glacial than of interglacial episodes) and in lateral area (greater land area at low than at high elevations) have opposing effects on lowland extinctions and the elevational pattern of species richness in the model--and perhaps in nature, as well.