An experimental test of Darwin's naturalization hypothesis

Phylogeny structures species' interactions in experimental ecological communities

Species' traits and interactions are products of evolutionary history. Despite the long-standing hypothesis that closely related species possess similar traits, and thus experience stronger competition, measuring the effect of evolutionary history on the ecology of natural communities remains challenging. We propose a novel framework to test whether phylogeny influences patterns of coexistence and abundance of species assemblages. In our approach, phylogenetic trees are used to parameterize species' interactions, which in turn determine the abundance of species in a given assemblage. We use likelihoods to score models parameterized with a given phylogeny, and contrast them with models built using random trees, allowing us to test whether phylogenetic information helps to predict species' abundances. Our statistical framework reveals that interactions are indeed structured by phylogeny in a large set of experimental plant communities. Our results confirm that evolutionary history can help predict, and potentially manage or conserve, the structure and function of complex ecological communities.

A phylogenomic perspective on interspecific competition

Evolutionary processes may have substantial impacts on community assembly, but evidence for phylogenetic relatedness as a determinant of interspecific interaction strength remains mixed. In this perspective, we consider a possible role for discordance between gene trees and species trees in the interpretation of phylogenetic signal in studies of community ecology. Modern genomic data show that the evolutionary histories of many taxa are better described by a patchwork of histories that vary along the genome rather than a single species tree. If a subset of genomic loci harbour trait-related genetic variation, then the phylogeny at these loci may be more informative of interspecific trait differences than the genome background. We develop a simple method to detect loci harbouring phylogenetic signal and demonstrate its application through a proof-of-principle analysis of Penicillium genomes and pairwise interaction strength. Our results show that phylogenetic signal that may be masked genome-wide could be detectable using phylogenomic techniques and may provide a window into the genetic basis for interspecific interactions.

Darwin's naturalization conundrum reconciled by changes of species interactions

Although phylogenetic distance between native and exotic species has a close link with their interactions, it is still unclear how environmental stresses and species interactions influence the relationship between phylogenetic distance and biological invasions. Here we assessed the effect of invader-native phylogenetic distance on the growth of the invader (Symphyotrichum subulatum) under three levels of drought (no, moderate, or intense drought). Under no drought, interspecific competition between close relatives was the dominant process and native communities more closely related to the invader showed higher resistance to invasion, supporting Darwin's naturalization hypothesis. In contrast, under intense drought, facilitation between close relatives by mutualism with arbuscular mycorrhizal fungi (AMF) became more important, and the invader became more successful in their more closely related native communities, supporting the preadaptation hypothesis. The colonization rate of AMF of the invader was higher in more closely related native communities regardless of the drought treatment, but it was only positively related to invader biomass under intense drought. Therefore, the shift of species interactions from competition to facilitation may be ascribed to the promotion of AMF to invasion occurring under intense drought, which leads to the effect of closely related natives on the invader shifting from negative to positive. Our results provide a new angle to resolve Darwin's naturalization conundrum from the change of species interactions along a stress gradient, and provide important clues for invasion management when species interactions change in response to global climatic change.

Spatial scales of competition and a growth-motility trade-off interact to determine bacterial coexistence

The coexistence of competing species is a long-lasting puzzle in evolutionary ecology research. Despite abundant experimental evidence showing that the opportunity for coexistence decreases as niche overlap increases between species, bacterial species and strains competing for the same resources are commonly found across diverse spatially heterogeneous habitats. We thus hypothesized that the spatial scale of competition may play a key role in determining bacterial coexistence, and interact with other mechanisms that promote coexistence, including a growth-motility trade-off. To test this hypothesis, we let two Pseudomonas putida strains compete at local and regional scales by inoculating them either in a mixed droplet or in separate droplets in the same Petri dish, respectively. We also created conditions that allow the bacterial strains to disperse across abiotic or fungal hyphae networks. We found that competition at the local scale led to competitive exclusion while regional competition promoted coexistence. When competing in the presence of dispersal networks, the growth-motility trade-off promoted coexistence only when the strains were inoculated in separate droplets. Our results provide a mechanism by which existing laboratory data suggesting competitive exclusion at a local scale is reconciled with the widespread coexistence of competing bacterial strains in complex natural environments with dispersal.

Phylogenetic Relationships and Disturbance Explain the Resistance of Different Habitats to Plant Invasions

Invasive alien plants have invaded various habitats, posing a threat to biodiversity. Several hypotheses have been proposed to explain the mechanisms of invasion, but few studies have considered the characteristics of the invaded communities and the effects of human interference in the invasion. In this study, we compared the invasibility of three different habitats: abandoned land, eucalyptus plantations, and natural secondary forests. We explored the effects of species diversity, phylogenetic diversity, and disturbance factors on the invasibility of different habitats. The results showed that the invasibility of abandoned land was the highest and the invasibility of the natural secondary forest was the lowest. Phylogenetic indicators affected the invasibility of abandoned land and eucalyptus plantations, and disturbance factors affected the invasibility of all three habitats, while the characteristics of the invaded communities had a weak impact. Our research provided supporting evidence for Darwin’s naturalization hypothesis and his disturbance hypothesis but found no relationship between biotic resistance and invasibility. This study indicated that the differences among habitats should be considered when we prove Darwin’s naturalization hypothesis in nature reserves.

Exotic fishes that are phylogenetically close but functionally distant to native fishes are more likely to establish

Since Darwin's time, degree of ecological similarity between exotic and native species has been assumed to affect the establishment success or failure of exotic species. However, a direct test of the effect of exotic-native similarity on establishment of exotics is scarce because of the difficulty in recognizing failures of species to establish in the field. Here, using a database on the establishment success and failure of exotic fish species introduced into 673 freshwater lakes, we evaluate the effect of similarity on the establishment of exotic fishes by combining phylogenetic and functional information. We illustrate that, relative to other biotic and abiotic factors, exotic-native phylogenetic and functional similarities were the most important correlates of exotic fish establishment. While phylogenetic similarity between exotic and resident fish species promoted successful establishment, functional similarity led to failure of exotics to become established. Those exotic species phylogenetically close to, but functionally distant from, native fishes were most likely to establish successfully. Our findings provide a perspective to reconcile Darwin's naturalization conundrum and suggest that, while phylogenetic relatedness allows exotic fish species to pre-adapt better to novel environments, they need to possess distinct functional traits to reduce competition with resident native fish species.

A test of Darwin's naturalization conundrum in birds reveals enhanced invasion success in the presence of close relatives

Biological invasions pose one of the most severe environmental challenges of the twenty-first century. A longstanding idea is that invasion risk is predictable based on the phylogenetic distance - and hence ecological resemblance - between non-native and native species. However, current evidence is contradictory. To explain these mixed results, it has been proposed that the effect is scale-dependent, with invasion inhibited by phylogenetic similarity at small spatial scales but enhanced at larger scales. Analyzing invasion outcomes in a global sample of bird communities, we find no evidence to support this hypothesis. Instead, our results suggest that invaders are locally more successful in the presence of closely related and ecologically similar species, at least in human-altered environments where the majority of invasions have occurred. Functional trait analyses further confirm that the ecological niches of invaders are phylogenetically conserved, supporting the notion that successful invasion in the presence of close relatives is driven by shared adaptations to the types of niches available in novel environments.

Mate choice errors may contribute to slow spread of an invasive Eurasian longhorn beetle in North America

Tetropium fuscum (Coleoptera: Cerambycidae) is a Eurasian longhorn beetle and forest pest that first became invasive to Nova Scotia, Canada around 1990. In the time since its introduction, T. fuscum has spread only about 150 km from its point of introduction. In its invasive range, T. fuscum co-exists with its congener Tetropium cinnamopterum. Although they are ecologically similar species, T. fuscum tends to infest healthier trees and has a smaller host range than T. cinnamopterum. If they successfully interbreed, this could lead to hybrid individuals that are more problematic than either parent species. On the other hand, if T. fuscum can make mating errors in the field, but is not producing hybrid offspring, then this waste of mating resources could help explain the slow spread of T. fuscum in North America. We conducted no-choice and choice mating experiments between T. fuscum and T. cinnamopterum males and females and determined that both T. fuscum and T. cinnamopterum males make mate-choice errors with heterospecific females in a laboratory setting. Our results suggest that mating errors may play a role in the slow spread of T. fuscum in North America.

Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms

Common garden experiments that inoculate a standardised growth medium with synthetic microbial communities (i.e. constructed from individual isolates or using dilution cultures) suggest that the ability of the community to resist invasions by additional microbial taxa can be predicted by the overall community productivity (broadly defined as cumulative cell density and/or growth rate). However, to the best of our knowledge, no common garden study has yet investigated the relationship between microbial community composition and invasion resistance in microcosms whose compositional differences reflect natural, rather than laboratory-designed, variation. We conducted experimental invasions of two bacterial strains (Pseudomonas fluorescens and Pseudomonas putida) into laboratory microcosms inoculated with 680 different mixtures of bacteria derived from naturally occurring microbial communities collected in the field. Using 16S rRNA gene amplicon sequencing to characterise microcosm starting composition, and high-throughput assays of community phenotypes including productivity and invader survival, we determined that productivity is a key predictor of invasion resistance in natural microbial communities, substantially mediating the effect of composition on invasion resistance. The results suggest that similar general principles govern invasion in artificial and natural communities, and that factors affecting resident community productivity should be a focal point for future microbial invasion experiments.

Phylogenetic and functional distinctiveness explain alien plant population responses to competition

Several invasion hypotheses predict a positive association between phylogenetic and functional distinctiveness of aliens and their performance, leading to the idea that distinct aliens compete less with their resident communities. However, synthetic pattern relationships between distinctiveness and alien performance and direct tests of competition as the driving mechanism have not been forthcoming. This is likely because different patterns are observed at different spatial grains, because functional trait and phylogenetic information are often incomplete, and because of the need for competition experiments that measure demographic responses across a variety of alien species that vary in their distinctiveness. We conduct a competitor removal experiment and parameterize matrix population and integral projection models for 14 alien plant species. More novel aliens compete less strongly with co-occurring species in their community, but these results dissipate at a larger spatial grain of investigation. Further, we find that functional traits used in conjunction with phylogeny improve our ability to explain competitive responses. Our investigation shows that competition is an important mechanism underlying the differential success of alien species.

Microhabitats are associated with diversity-productivity relationships in freshwater bacterial communities

Eukaryotic communities commonly display a positive relationship between biodiversity and ecosystem function (BEF) but the results have been mixed when assessed in bacterial communities. Habitat heterogeneity, a factor in eukaryotic BEFs, may explain these variable observations but it has not been thoroughly evaluated in bacterial communities. Here, we examined the impact of habitat on the relationship between diversity assessed based on the (phylogenetic) Hill diversity metrics and heterotrophic productivity. We sampled co-occurring free-living (more homogenous) and particle-associated (more heterogeneous) bacterial habitats in a freshwater, estuarine lake over three seasons: spring, summer and fall. There was a strong, positive, linear relationship between particle-associated bacterial richness and heterotrophic productivity that strengthened when considering dominant taxa. There were no observable BEF trends in free-living bacterial communities for any diversity metric. Biodiversity, richness and Inverse Simpson's index, were the best predictors of particle-associated production whereas pH was the best predictor of free-living production. Our findings show that heterotrophic productivity is positively correlated with the effective number of taxa and that BEF relationships are associated with microhabitats. These results add to the understanding of the highly distinct contributions to diversity and functioning contributed by bacteria in free-living and particle-associated habitats.

Stochastic processes govern invasion success in microbial communities when the invader is phylogenetically close to resident bacteria

Despite recent efforts in identifying the determinants of invasion in microbial communities, experimental observations across different ecosystems are inconclusive. While relationships between resident community diversity and invasion success are often noted, community diversity says little about community assembly processes. Community assembly processes may provide a more inclusive framework to explain-and potentially prevent or facilitate-invasion. Here we let replicate nitrite-oxidizing bacterial guilds assemble under different conditions from a natural source community and study their compositional patterns to infer the relative importance of the assembly processes. Then, an invader strain from that same guild was introduced at one of three propagule pressures. We found no significant correlation between community diversity and invasion success. Instead, we observed that the effect of selection on invasion success was surpassed by the effect of drift, as inferred from the substantial influence of propagule pressure on invasion success. This dominance of drift can probably be generalized to other invasion cases with high phylogenetic similarity between invader and resident community members. In these situations, our results suggest that attempting to modulate the invasibility of a community by altering its diversity is futile because stochastic processes determine the invasion outcome. Increasing or reducing propagule pressure is then deemed the most efficient avenue to enhance or limit invasion success.

The influence of ecological and geographic limits on the evolution of species distributions and diversity

The role of ecological limits in regulating the distribution and diversification of species remains controversial. Although such limits must ultimately arise from constraints on local species coexistence, this spatial context is missing from most macroevolutionary models. Here, we develop a stochastic, spatially explicit model of species diversification to explore the phylogenetic and biogeographic patterns expected when local diversity is bounded. We show how local ecological limits, by regulating opportunities for range expansion and thus rates of speciation and extinction, lead to temporal slowdowns in diversification and predictable differences in equilibrium diversity between regions. However, our models also show that even when regions have identical diversity limits, the dynamics of diversification and total number of species supported at equilibrium can vary dramatically depending on the relative size of geographic and local ecological niche space. Our model predicts that small regions with higher local ecological limits support a higher standing diversity and more balanced phylogenetic trees than large geographic areas with more stringent constraints on local coexistence. Our findings highlight how considering the spatial context of diversification can provide new insights into the role of ecological limits in driving variation in biodiversity across space, time, and clades.

Emergent niche structuring leads to increased differences from neutrality in species abundance distributions

Species abundance distributions must reflect the dynamic processes involved in community assembly, but whether and when specific processes lead to distinguishable signals is not well understood. Biodiversity and species abundances may be shaped by a variety of influences, but particular attention has been paid to competition, which can involve neutral dynamics, where competitor abundances are governed only by demographic stochasticity and immigration, and dynamics driven by trait differences that enable stable coexistence through the formation of niches. Key recent studies of the species abundance patterns of communities with niches employ simple models with pre-imposed niche structure. These studies suggest that species abundance distributions are insensitive to the relative contributions of niche and neutral processes, especially when diversity is much higher than the number of niches. Here we analyze results from a stochastic population model with competition driven by trait differences. With this model, niche structure emerges as clumps of species that persist along the trait axis, and leads to more substantial differences from neutral species abundance distributions than have been previously shown. We show that heterogeneity in "between-niche" interaction strength (i.e., in the strength of competition between species in different niches) plays the dominant role in shaping the species abundances along the trait axis, acting as a biotic filter favoring species at the centers of niches. Furthermore, we show that heterogeneity in "within-niche" interactions (i.e., in the competition between species in the same niche) counteracts the influence of heterogeneity in "between-niche" interactions on the SAD to some degree. Our results suggest that competitive interactions that produce niches can also influence the shapes of SADs.

Preadaptation and Naturalization of Nonnative Species: Darwin's Two Fundamental Insights into Species Invasion

Predicting which nonnative species become invasive is critical for their successful management, and Charles Darwin provided predictions based on species' relatedness. However, Darwin provided two opposing predictions about the relatedness of introduced nonnatives to indigenous species. First, environmental fit is the dominant factor determining invader success; thus, we should expect that invasive species are closely related to local native residents. Alternatively, if competition is important, we should expect successful invaders are distantly related to the native residents. These opposing expectations are referred to as Darwin's naturalization conundrum. The results of studies that examine nonnative species relatedness to natives are largely inconsistent. This inconsistency arises from the fact that studies occur at different spatial and temporal scales, and at different stages of invasion, and so implicitly examine different mechanisms. Further, while species have evolved ecological differences, the mode and tempo of evolution can affect species' differences, complicating the predictions from simple hypotheses. We outline unanswered questions and provide guidelines for collecting the data required to test competing hypotheses.

Different effects of invader-native phylogenetic relatedness on invasion success and impact: a meta-analysis of Darwin's naturalization hypothesis

Darwin's naturalization hypothesis (DNH), which predicts that alien species more distantly related to native communities are more likely to naturalize, has received much recent attention. The mixed findings from empirical studies that have tested DNH, however, seem to defy generalizations. Using meta-analysis to synthesize results of existing studies, we show that the predictive power of DNH depends on both the invasion stage and the spatial scale of the studies. Alien species more closely related to natives tended to be less successful at the local scale, supporting DNH; invasion success, however, was unaffected by alien-native relatedness at the regional scale. On the other hand, alien species with stronger impacts on native communities tended to be more closely related to natives at the local scale, but less closely related to natives at the regional scale. These patterns are generally consistent across different ecosystems, taxa and investigation methods. Our results revealed the different effects of invader-native relatedness on invader success and impact, suggesting the operation of different mechanisms across invasion stages and spatial scales.

Phylogenetic context determines the role of competition in adaptive radiation

Understanding ecological mechanisms regulating the evolution of biodiversity is of much interest to ecologists and evolutionary biologists. Adaptive radiation constitutes an important evolutionary process that generates biodiversity. Competition has long been thought to influence adaptive radiation, but the directionality of its effect and associated mechanisms remain ambiguous. Here, we report a rigorous experimental test of the role of competition on adaptive radiation using the rapidly evolving bacterium Pseudomonas fluorescens SBW25 interacting with multiple bacterial species that differed in their phylogenetic distance to the diversifying bacterium. We showed that the inhibitive effect of competitors on the adaptive radiation of P. fluorescens decreased as their phylogenetic distance increased. To explain this phylogenetic dependency of adaptive radiation, we linked the phylogenetic distance between P. fluorescens and its competitors to their niche and competitive fitness differences. Competitive fitness differences, which showed weak phylogenetic signal, reduced P. fluorescens abundance and thus diversification, whereas phylogenetically conserved niche differences promoted diversification. These results demonstrate the context dependency of competitive effects on adaptive radiation, and highlight the importance of past evolutionary history for ongoing evolutionary processes.

Biodiversity maintenance may be lower under partial niche differentiation than under neutrality

Niche differentiation is normally regarded as a key promoter of species coexistence in competitive systems. One might therefore expect that relative to neutral assemblages, niche-differentiated communities should support more species with longer persistence and lower probability of extinction. Here we compare stochastic niche and neutral dynamics in simulated assemblages, and find that when local dynamics combine with immigration from a regional pool, the effect of niches can be more complex. Trait variation that lessens competition between species will not necessarily give all immigrating species their own niche to occupy. Such partial niche differentiation protects certain species from local extinction, but precipitates exclusion of others. Differences in regional abundances and intrinsic growth rates have similar impacts on persistence times as niche differentiation, and therefore blur the distinction between niche and neutral dynamical patterns-although niche dynamics will influence which species persist longer. Ultimately, unless the number of niches available to species is sufficiently high, niches may actually heighten extinction rates and lower species richness and local persistence times. Our results help make sense of recent observations of community dynamics, and point to the dynamical observations needed to discern the influence of niche differentiation.

Dissecting spatiotemporal patterns of functional diversity through the lens of Darwin's naturalization conundrum

Darwin's naturalization conundrum describes the paradigm that community assembly is regulated by two opposing processes, environmental filtering and competitive interactions, which predict both similarity and distinctiveness of species to be important for establishment. Our goal is to use long-term, large-scale, and high-resolution temporal data to examine diversity patterns over time and assess whether environmental filtering or competition plays a larger role in regulating community assembly processes. We evaluated Darwin's naturalization conundrum and how functional diversity has changed in the Laurentian Great Lakes fish community from 1870 to 2010, which has experienced frequent introductions of non-native species and extirpations of native species. We analyzed how functional diversity has changed over time by decade from 1870 to 2010 at three spatial scales (regional, lake, and habitat) to account for potential noninteractions between species at the regional and lake level. We also determined which process, environmental filtering or competitive interactions, is more important in regulating community assembly and maintenance by comparing observed patterns to what we would expect in the absence of an ecological mechanism. With the exception of one community, all analyses show that functional diversity and species richness has increased over time and that environmental filtering regulates community assembly at the regional level. When examining functional diversity at the lake and habitat level, the regulating processes become more context dependent. This study is the first to examine diversity patterns and Darwin's conundrum by integrating long-term, large-scale, and high-resolution temporal data at multiple spatial scales. Our results confirm that Darwin's conundrum is highly context dependent.

Propagule pressure increase and phylogenetic diversity decrease community's susceptibility to invasion

BACKGROUND

Invasions pose a large threat to native species, but the question of why some species are more invasive, and some communities more prone to invasions than others, is far from solved. Using 10 different three-species bacterial communities, we tested experimentally if the phylogenetic relationships between an invader and a resident community and the propagule pressure affect invasion probability.

RESULTS

We found that greater diversity in phylogenetic distances between the members of resident community and the invader lowered invasion success, and higher propagule pressure increased invasion success whereas phylogenetic distance had no clear effect. In the later stages of invasion, phylogenetic diversity had no effect on invasion success but community identity played a stronger role.

CONCLUSIONS

Taken together, our results emphasize that invasion success does not depend only on propagule pressure, but also on the properties of the community members. Our results thus indicate that invasion is a process where both invader and residing community characters act in concert.

Effectiveness of ecological rescue for altered soil microbial communities and functions

Soil ecosystems worldwide are subjected to marked modifications caused by anthropogenic disturbances and global climate change, resulting in microbial diversity loss and alteration of ecosystem functions. Despite the paucity of studies, restoration ecology provides an appropriate framework for testing the potential of manipulating soil microbial communities for the recovery of ecosystem functioning. We used a reciprocal transplant design in experimentally altered microbial communities to investigate the effectiveness of introducing microbial communities in degraded soil ecosystems to restore N-cycle functioning. Microbial diversity loss resulted in alternative compositional states associated with impaired N-cycle functioning. Here, the addition of complex microbial communities to these altered communities revealed a pivotal role of deterministic community assembly processes. The diversity of some alternative compositional states was successfully increased but without significant restoration of soil N-cycle functioning. However, in the most degraded alternative state, the introduction of new microbial communities caused an overall decrease in phylogenetic diversity and richness. The successful soil colonization by newly introduced species for some compositional states indicates that priority effects could be overridden when attempting to manipulate microbial communities for soil restoration. Altogether, our result showed consistent patterns within restoration treatments with minor idiosyncratic effects. This suggests the predominance of deterministic processes and the predictability of restoration trajectories, which could be used to guide the effective management of microbial community assemblages for ecological restoration of soils.

A conceptual framework for invasion in microbial communities

There is a growing interest in controlling-promoting or avoiding-the invasion of microbial communities by new community members. Resource availability and community structure have been reported as determinants of invasion success. However, most invasion studies do not adhere to a coherent and consistent terminology nor always include rigorous interpretations of the processes behind invasion. Therefore, we suggest that a consistent set of definitions and a rigorous conceptual framework are needed. We define invasion in a microbial community as the establishment of an alien microbial type in a resident community and argue how simple criteria to define aliens, residents, and alien establishment can be applied for a wide variety of communities. In addition, we suggest an adoption of the community ecology framework advanced by Vellend (2010) to clarify potential determinants of invasion. This framework identifies four fundamental processes that control community dynamics: dispersal, selection, drift and diversification. While selection has received ample attention in microbial community invasion research, the three other processes are often overlooked. Here, we elaborate on the relevance of all four processes and conclude that invasion experiments should be designed to elucidate the role of dispersal, drift and diversification, in order to obtain a complete picture of invasion as a community process.

Phylogenetic relatedness and leaf functional traits, not introduced status, influence community assembly

Considerable debate focuses on whether invasive species establish and become abundant by being functionally and phylogenetically distinct from native species, leading to a host of invasion-specific hypotheses of community assembly. Few studies, however, have quantitatively assessed whether similar patterns of phylogenetic and functional similarity explain local abundance of both native and introduced species, which would suggest similar assembly mechanisms regardless of origin. Using a chronosequence of invaded temperate forest stands, we tested whether the occurrence and abundance of both introduced and native species were predicted by phylogenetic relatedness, functional overlap, and key environmental characteristics including forest age. Environmental filtering against functionally and phylogenetically distinct species strongly dictated the occurrence and abundance of both introduced and native species, with slight modifications of these patterns according to forest age. Thus, once functional and evolutionary novelty were quantified, introduced status provided little information about species' presence or abundance, indicating largely similar sorting mechanisms for both native and introduced species.

Fungal communities as an experimental approach to Darwin's naturalization hypothesis

Darwin's naturalization hypothesis suggests that the success of an invasive species will be lower when colonizing communities are formed by phylogenetically related rather than unrelated species due to increased competition. Although microbial invasions are involved in both natural and anthropogenic processes, factors affecting the success of microbial invaders are unknown. A biological invasion assay was designed using Trichoderma cf. harzianum as the invader and two types of recipient communities assembled in microcosm assays: communities phylogenetically related to the invader, and communities phylogenetically unrelated to it. Both types of communities were invaded by T. cf. harzianum, and the success of colonization was monitored by qPCR; its effect on the genetic structure of recipient fungal communities was then assessed by DGGE profiles. T. cf. harzianum established itself in both communities, reaching 1000-10,000 times higher copy numbers in the non-related communities. However, invader establishment does not affect the structure of the invaded communities. These results suggest that the composition of recipient communities and their phylogenetic relationship to the invader affect the success of colonization by T. cf. harzianum. While this approach represents a very simplified assay, these microcosms enable an experimental test of Darwin's hypothesis in order to understand the biological invasion process in microbial communities.

Ecology of bacteria in the human gastrointestinal tract--identification of keystone and foundation taxa

BACKGROUND

Determining ecological roles of community members and the impact of specific taxa on overall biodiversity in the gastrointestinal (GI) microbiota is of fundamental importance. A step towards a systems-level understanding of the GI microbiota is characterization of biotic interactions. Community time series analysis, an approach based on statistical analysis of changing population abundances within a single system over time, is needed in order to say with confidence that one population is affecting the dynamics of another.

RESULTS

Here, we characterize biotic interaction structures and define ecological roles of major bacterial groups in four healthy individuals by analysing high-resolution, long-term (>180 days) GI bacterial community time series. Actinobacteria fit the description of a keystone taxon since they are relatively rare, but have a high degree of ecological connectedness, and are positively correlated with diversity both within and between individuals. Bacteriodetes were found to be a foundation taxon in that they are numerically dominant and interact extensively, in particular through positive interactions, with other taxa. Although community structure, diversity and biotic interaction patterns were specific to each individual, we observed a strong tendency towards more intense competition within than between phyla. This is in agreement with Darwin's limiting similarity hypothesis as well as a published biotic interaction model of the GI microbiota based on reverse ecology. Finally, we link temporal enterotype switching to a reciprocal positive interaction between two key genera.

CONCLUSIONS

In this study, we identified ecological roles of key taxa in the human GI microbiota and compared our time series analysis results with those obtained through a reverse ecology approach, providing further evidence in favour of the limiting similarity hypothesis first put forth by Darwin. Larger longitudinal studies are warranted in order to evaluate the generality of basic ecological concepts as applied to the GI microbiota, but our results provide a starting point for achieving a more profound understanding of the GI microbiota as an ecological system.

Evolutionary relatedness does not predict competition and co-occurrence in natural or experimental communities of green algae

The competition-relatedness hypothesis (CRH) predicts that the strength of competition is the strongest among closely related species and decreases as species become less related. This hypothesis is based on the assumption that common ancestry causes close relatives to share biological traits that lead to greater ecological similarity. Although intuitively appealing, the extent to which phylogeny can predict competition and co-occurrence among species has only recently been rigorously tested, with mixed results. When studies have failed to support the CRH, critics have pointed out at least three limitations: (i) the use of data poor phylogenies that provide inaccurate estimates of species relatedness, (ii) the use of inappropriate statistical models that fail to detect relationships between relatedness and species interactions amidst nonlinearities and heteroskedastic variances, and (iii) overly simplified laboratory conditions that fail to allow eco-evolutionary relationships to emerge. Here, we address these limitations and find they do not explain why evolutionary relatedness fails to predict the strength of species interactions or probabilities of coexistence among freshwater green algae. First, we construct a new data-rich, transcriptome-based phylogeny of common freshwater green algae that are commonly cultured and used for laboratory experiments. Using this new phylogeny, we re-analyse ecological data from three previously published laboratory experiments. After accounting for the possibility of nonlinearities and heterogeneity of variances across levels of relatedness, we find no relationship between phylogenetic distance and ecological traits. In addition, we show that communities of North American green algae are randomly composed with respect to their evolutionary relationships in 99% of 1077 lakes spanning the continental United States. Together, these analyses result in one of the most comprehensive case studies of how evolutionary history influences species interactions and community assembly in both natural and experimental systems. Our results challenge the generality of the CRH and suggest it may be time to re-evaluate the validity and assumptions of this hypothesis.

Intraspecies competition for niches in the distal gut dictate transmission during persistent Salmonella infection

In order to be transmitted, a pathogen must first successfully colonize and multiply within a host. Ecological principles can be applied to study host-pathogen interactions to predict transmission dynamics. Little is known about the population biology of Salmonella during persistent infection. To define Salmonella enterica serovar Typhimurium population structure in this context, 129SvJ mice were oral gavaged with a mixture of eight wild-type isogenic tagged Salmonella (WITS) strains. Distinct subpopulations arose within intestinal and systemic tissues after 35 days, and clonal expansion of the cecal and colonic subpopulation was responsible for increases in Salmonella fecal shedding. A co-infection system utilizing differentially marked isogenic strains was developed in which each mouse received one strain orally and the other systemically by intraperitoneal (IP) injection. Co-infections demonstrated that the intestinal subpopulation exerted intraspecies priority effects by excluding systemic S. Typhimurium from colonizing an extracellular niche within the cecum and colon. Importantly, the systemic strain was excluded from these distal gut sites and was not transmitted to naïve hosts. In addition, S. Typhimurium required hydrogenase, an enzyme that mediates acquisition of hydrogen from the gut microbiota, during the first week of infection to exert priority effects in the gut. Thus, early inhibitory priority effects are facilitated by the acquisition of nutrients, which allow S. Typhimurium to successfully compete for a nutritional niche in the distal gut. We also show that intraspecies colonization resistance is maintained by Salmonella Pathogenicity Islands SPI1 and SPI2 during persistent distal gut infection. Thus, important virulence effectors not only modulate interactions with host cells, but are crucial for Salmonella colonization of an extracellular intestinal niche and thereby also shape intraspecies dynamics. We conclude that priority effects and intraspecies competition for colonization niches in the distal gut control Salmonella population assembly and transmission.

Differences in evolutionary history translate into differences in invasion success of alien mammals in South Africa

Attempts to investigate the drivers of invasion success are generally limited to the biological and evolutionary traits distinguishing native from introduced species. Although alien species introduced to the same recipient environment differ in their invasion intensity – for example, some are “strong invaders”; others are “weak invaders” – the factors underlying the variation in invasion success within alien communities are little explored. In this study, we ask what drives the variation in invasion success of alien mammals in South Africa. First, we tested for taxonomic and phylogenetic signal in invasion intensity. Second, we reconstructed predictive models of the variation in invasion intensity among alien mammals using the generalized linear mixed-effects models. We found that the family Bovidae and the order Artiodactyla contained more “strong invaders” than expected by chance, and that such taxonomic signal did not translate into phylogenetic selectivity. In addition, our study indicates that latitude, gestation length, social group size, and human population density are only marginal determinant of the variation in invasion success. However, we found that evolutionary distinctiveness – a parameter characterising the uniqueness of each alien species – is the most important predictive variable. Our results indicate that the invasive behavior of alien mammals may have been “fingerprinted” in their evolutionary past, and that evolutionary history might capture beyond ecological, biological and life-history traits usually prioritized in predictive modeling of invasion success. These findings have applicability to the management of alien mammals in South Africa.

Evaluating Darwin's naturalization hypothesis in experimental plant assemblages: phylogenetic relationships do not determine colonization success

Darwin's naturalization hypothesis (DNH) proposes that colonization is less likely when the colonizing species is related to members of the invaded community, because evolutionary closeness intensifies competition among species that share similar resources. Studies that have evaluated DNH from correlational evidence have yielded controversial results with respect to its occurrence and generality. In the present study we carried out a set of manipulative experiments in which we controlled the phylogenetic relatedness of one colonizing species (Lactuca sativa) with five assemblages of plants (the recipient communities), and evaluated the colonizing success using five indicators (germination, growth, flowering, survival, and recruitment). The evolutionary relatedness was calculated as the mean phylogenetic distance between Lactuca and the members of each assemblage (MPD) and by the mean phylogenetic distance to the nearest neighbor (MNND). The results showed that the colonization success of Lactuca was not affected by MPD or MNND values, findings that do not support DNH. These results disagree with experimental studies made with communities of microorganisms, which show an inverse relation between colonization success and phylogenetic distances. We suggest that these discrepancies may be due to the high phylogenetic distance used, since in our experiments the colonizing species (Lactuca) was a distant relative of the assemblage members, while in the other studies the colonizing taxa have been related at the congeneric and conspecific levels. We suggest that under field conditions the phylogenetic distance is a weak predictor of competition, and it has a limited role in determining colonization success, contrary to prediction of the DNH. More experimental studies are needed to establish the importance of phylogenetic distance between colonizing species and invaded community on colonization success.

Evolutionary history and the strength of species interactions: testing the phylogenetic limiting similarity hypothesis

A longstanding concept in community ecology is that closely related species compete more strongly than distant relatives. Ecologists have invoked this "limiting similarity hypothesis" to explain patterns in the structure and function of biological communities and to inform conservation, restoration, and invasive-species management. However, few studies have empirically tested the validity of the limiting similarity hypothesis. Here we report the results of a laboratory microcosm experiment in which we used a model system of 23 common, co-occurring North American freshwater green algae to quantify the strength of 216 pairwise species' interactions (the difference in population density when grown alone vs. in the presence of another species) along a manipulated gradient of evolutionary relatedness (phylogenetic distance, as the sum of branch lengths separating species on a molecular phylogeny). Interspecific interactions varied widely in these bicultures of phytoplankton, ranging from strong competition (ratio of relative yield in polyculture vs. monoculture << 1) to moderate facilitation (relative yield > 1). Yet, we found no evidence that the strength of species' interactions was influenced by their evolutionary relatedness. There was no relationship between phylogenetic distance and the average, minimum (inferior competitor), nor maximum (superior competitor) interaction strength across all biculture communities (respectively, P = 0.19, P = 0.17, P = 0.14; N = 428). When we examined each individual species, only 17% of individual species' interactions strengths varied as a function of phylogenetic distance, and none of these relationships remained significant after Bonferoni correction for multiple tests (N = 23). Last, when we grouped interactions into five qualitatively different types, the frequency of these types was not related to phylogenetic distance among species pairs (F4,422 = 1.63, P = 0.15). Our empirical study adds to several others that suggest the biological underpinnings of competition may not be evolutionarily conserved, and thus, ecologists may need to re-evaluate the previously assumed generality of the limiting similarity hypothesis.

Functional and phylogenetic similarity of alien plants to co-occurring natives

Over the years, several arguments have been proposed to explain the invasibility of a given community based on the properties of the recipient community. Here, I assessed whether the balance between native species' phylogenetic and functional variability determines vulnerability to invasion. I explored this hypothesis using a consensus phylogenetic tree and a database of leaf, height, and seed traits of alien and native species co-occurring over 83 sites worldwide. An analysis of contrasts between aliens and natives indicates that aliens are as phylogenetically close to the incumbent native community as natives are among themselves (aliens are nested within the native community phylogeny), but functionally distinct to the native community (aliens are more functionally distant to the community of native taxa than natives are among themselves). These contrasting trends are consistent for different comparison criteria (comparisons to all natives or to the nearest native) and comparisons both within and across communities, habitats, and continents. Furthermore, aliens are more functionally divergent than the native community and the closest native relative in both phylogenetically poor and rich communities. The phylogenetic similarity and functional distinctiveness of aliens with respect to the incumbent native community may explain why certain species succeed in some communities and not others. This is a step forward in resolving the long-standing debate on the role diversity--both phylogenetic and functional--plays in determining the success of introduced plants.

Biologic interactions determining geographic range size: a one species response to phylogenetic community structure

Range size variation in closely related species suggests different responses to biotic and abiotic heterogeneity across large geographic regions. Species turnover generates a wide spectrum of species assemblages, resulting in different competition intensities among taxa, creating restrictions as important as environmental constraints. We chose to adopt the widely used phylogenetic relatedness (NRI) measurement to define a metric that depicts competition strength (via phylogenetic similarity), which one focal species confronts in its environment. This new approach (NRI_focal) measures the potential of the community structure effect over performance of a single species. We chose two ecologically similar Peucaea sparrows, which co-occur and have highly dissimilar range size to test whether the population response to competition intensity is different between species. We analyzed the correlation between both Peucaea species population sizes and NRI_focal using data from point counts. Results indicated that the widespread species population size was not associated with NRI_focal, whereas the population of restricted-sized species exhibited a negative relationship with competition intensity. Consequently, a species' sensitivity to competition might be a limiting factor to range expansion, which provides new insights into geographic range analysis and community ecology.

Historical contingency in species interactions: towards niche-based predictions

The way species affect one another in ecological communities often depends on the order of species arrival. The magnitude of such historical contingency, known as priority effects, varies across species and environments, but this variation has proven difficult to predict, presenting a major challenge in understanding species interactions and consequences for community structure and function. Here, we argue that improved predictions can be achieved by decomposing species' niches into three components: overlap, impact and requirement. Based on classic theories of community assembly, three hypotheses that emphasise related, but distinct influences of the niche components are proposed: priority effects are stronger among species with higher resource use overlap; species that impact the environment to a greater extent exert stronger priority effects; and species whose growth rate is more sensitive to changes in the environment experience stronger priority effects. Using nectar-inhabiting microorganisms as a model system, we present evidence that these hypotheses complement the conventional hypothesis that focuses on the role of environmental harshness, and show that niches can be twice as predictive when separated into components. Taken together, our hypotheses provide a basis for developing a general framework within which the magnitude of historical contingency in species interactions can be predicted.