Article

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

May 2014
Ecology 95(5)

DOI:10.1890/13-0986.1

Authors:

Markos Alexandrou

University of California, Santa Barbara

Todd Oakley

University of California, Santa Barbara

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 pair-wise 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 (relative yield in poly: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). Lastly, when we grouped interactions into five qualitatively different types, the frequency of these types was not related to phylogenetic distance among species pairs (F = 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.

Phylogenetic distance does not predict competition in green algal communities

Article

Full-text available

Jul 2015

Biologists have held the tenet that closely related species compete more strongly with each other than with distant relatives since 1859, when Darwin observed that close relatives seldom co-occur in nature and suggested it was because they competitively exclude one another. The expectation that close relatives experience greater competition than distant relatives has become known as the ''competition-relatedness hypothesis (CRH).'' The CRH is predicated on the assumption that closely related species are more likely to have similar resource requirements than distant relatives, and thus, compete more strongly for limited resources. While this assumption has been popular because it is intuitive, it has also been subject to relatively little experimentation. Over the past decade, a growing number of CRH studies have arrived at divergent conclusions showing that the strength of competitive interactions can increase, decrease, or be independent of evolutionary relatedness. Most of these studies have focused on measuring competition among species pairs as opposed to competition experienced by species when part of whole communities. We tested whether the CRH holds in communities where individual species experience interactions with a variety of other taxa, which we call the 'resident community'. We performed a laboratory mesocosm study using communities of eight species of freshwater green algae whose evolutionary relationships were quantified using a recently developed multi-gene molecular phylogeny of 59 North American green algae. We grew species alone and in various combinations in polyculture so that we could measure each species' sensitivity to competition (reduction in intrinsic growth rate when grown alone vs. with a resident community), relative yield, and competitive release (proportional change in biomass of a species when grown in a resident community missing one competitor vs. in a community with all possible competitors). While each of these metrics consistently revealed a prevalence of competitive interactions among the algal species, none were predicted by the relatedness of a species to a resident community. This suggests that the results of prior pairwise studies refuting the competition-relatedness hypothesis for green algae can be extended to larger resident communities in which more complex ecological interactions possibly occur.

Phylogenetic and functional mechanisms of direct and indirect interactions among alien and native plants

Article

Mar 2016
J ECOL

Disentangling direct and indirect interactions among alien and native plants is essential to understanding the success of alien plants in multi-species communities, but studies have only focused on direct pairwise interactions. Moreover, it is also essential to explore phylogenetic and functional mechanisms driving these interactions. 2.In a greenhouse experiment, we selected nine groups of alien and native plant species from the herbaceous flora of Germany to disentangle their direct and indirect interactions. Each group had an alien (A) that is common or rare in Germany (i.e. non-native range), two natives that are phylogenetically closely related (Nclose) and distantly related (Ndist) to A respectively, and a distantly related “target” native (T). We grew the four species of each group alone, and in two-species and three-species combinations. Specifically, we tested whether competition is greater between A and Nclose than between A and Ndist, whether presence of Nclose rather than Ndist indirectly alleviates competition of A on T, and whether these interaction patterns depend on commonness of A. Moreover, we tested how intensity of these interactions is explained by phylogenetic distance, functional traits (height, seed mass, SLA, leaf size, specific root length, leaf area ratio, root length ratio (root length/plant mass), shoot weight ratio) and traits-based functional distance. 3.We found A had stronger competition on Nclose than on Ndist. In turn, A was more suppressed by Nclose than by Ndist, but this was only true for rare rather than common A. The presence of Ndist rather than Nclose indirectly reduced competition of A on T. The intensity of the interactions was not explained by phylogenetic or functional distance, but by some of the functional traits. Specifically, a plant experienced stronger competition when it was shorter and had smaller leaves and lower shoot weight ratio, and when its neighbors were taller, had greater SLA, leaf area ratio and shoot weight ratio, and had a lower root length ratio. 4.Synthesis. Functional traits can help explain competitive interactions. While direct competition tended to be stronger between more closely related alien and native plants, this did not indirectly facilitate other co-occurring native plants. This article is protected by copyright. All rights reserved.

Regional- and Local-scale Drivers of Establishment and Invasion Success of Alien Plants

Thesis

Full-text available

Jan 2015

Yanhao Feng

Common Ancestry Is a Poor Predictor of Competitive Traits in Freshwater Green Algae

Article

Full-text available

Sep 2015
PLOS ONE

Phytoplankton species traits have been used to successfully predict the outcome of competition, but these traits are notoriously laborious to measure. If these traits display a phylogenetic signal, phylogenetic distance (PD) can be used as a proxy for trait variation. We provide the first investigation of the degree of phylogenetic signal in traits related to competition in freshwater green phytoplankton. We measured 17 traits related to competition and tested whether they displayed a phylogenetic signal across a molecular phylogeny of 59 species of green algae. We also assessed the fit of five models of trait evolution to trait variation across the phylogeny. There was no significant phylogenetic signal for 13 out of 17 ecological traits. For 7 traits, a non-phylogenetic model provided the best fit. For another 7 traits, a phylogenetic model was selected, but parameter values indicated that trait variation evolved recently, diminishing the importance of common ancestry. This study suggests that traits related to competition in freshwater green algae are not generally well-predicted by patterns of common ancestry. We discuss the mechanisms by which the link between phylogenetic distance and phenotypic differentiation may be broken.

Phylogenetic distance does not predict competition in green algal communities

Article

Full-text available

Jul 2016

Markos Alexandrou

Biologists have held the tenet that closely related species compete more strongly with each other than with distant relatives since 1859, when Darwin observed that close relatives seldom co-occur in nature and suggested it was because they competitively exclude one another. The expectation that close relatives experience greater competition than distant relatives has become known as the ‘‘competition- relatedness hypothesis (CRH).’’ The CRH is predicated on the assumption that closely related species are more likely to have similar resource requirements than distant relatives, and thus, compete more strongly for limited resources. While this assumption has been popular because it is intuitive, it has also been subject to relatively little experimentation. Over the past decade, a growing number of CRH studies have arrived at divergent conclusions showing that the strength of competitive interactions can increase, decrease, or be independent of evolutionary relatedness. Most of these studies have focused on measuring competition among species pairs as opposed to competition experienced by species when part of whole communities. We tested whether the CRH holds in communities where individual species experience interactions with a variety of other taxa, which we call the ‘resident community’. We performed a laboratory mesocosm study using communities of eight species of freshwater green algae whose evolutionary relationships were quantified using a recently developed multi-gene molecular phylogeny of 59 North American green algae. We grew species alone and in various combinations in polyculture so that we could measure each species’ sensitivity to competition (reduction in intrinsic growth rate when grown alone vs. with a resident community), relative yield, and competitive release (proportional change in biomass of a species when grown in a resident community missing one competitor vs. in a community with all possible competitors). While each of these metrics consistently revealed a prevalence of competitive interactions among the algal species, none were predicted by the relatedness of a species to a resident community. This suggests that the results of prior pairwise studies refuting the competition-relatedness hypothesis for green algae can be extended to larger resident communities in which more complex ecological interactions possibly occur.

Biodiversity and disease risk in an algal biofuel system: An experimental test in outdoor ponds using a before-after-control-impact (BACI) design

Article

Apr 2022
PLOS ONE

For outdoor cultivation of algal feedstocks to become a commercially viable and sustainable option for biofuel production, algal cultivation must maintain high yields and temporal stability in environmentally variable outdoor ponds. One of the main challenges is mitigating disease outbreaks that leads to culture crashes. Drawing on predictions from the 'dilution effect' hypothesis, in which increased biodiversity is thought to reduce disease risk in a community, a teste of whether algal polycultures would reduce disease risk and improve feedstock production efficiencies compared to monocultures was performed. While the positive benefits of biodiversity on disease risk have been demonstrated in various systems, to the best of our knowledge this is the first test in an algal biofuel system. Here, the results a before-after-control-impact (BACI) experimental design to compare mean monoculture (control) and polyculture (impact) yield, stability, and productivity before and after fungal infection when grown in 400-L outdoor raceway ponds are presented. It has been found that polycultures did not experience a reduction in disease risk compared to monocultures or differ in production efficiencies throughout the course of the 43-day experiment. These results show that polyculture feedstocks can maintain similar levels of productivity, stability, and disease resistance to that of a monoculture. Determining whether these results are generalizable or represent one case study requires additional outdoor experiments using a larger variety of host and pathogen species.

Effects of taxon sampling and tree reconstruction methods on phylodiversity metrics

Article

Full-text available

Aug 2019

The amount and patterns of phylodiversity in a community are often used to draw inferences about the local and historical factors affecting community assembly and can be used to prioritize communities and locations for conservation. Because measures of phylodiversity are based on the topology and branch lengths of phylogenetic trees, which are affected by the number and diversity of taxa in the tree, these analyses may be sensitive to changes in taxon sampling and tree reconstruction methods. To investigate the effects of taxon sampling and tree reconstruction methods on measures of phylodiversity, we investigated the community phylogenetics of the Ordway‐Swisher Biological Station (Florida), which is home to over 600 species of vascular plants. We studied the effects of (a) the number of taxa included in the regional phylogeny; (b) random versus targeted sampling of species to assemble the regional species pool; (c) including only species from specific clades rather than broad sampling; (d) using trees reconstructed directly for the taxa under study compared to trees pruned from a larger reconstructed tree; and (e) using phylograms compared to chronograms. We found that including more taxa in a study increases the likelihood of observing significantly nonrandom phylogenetic patterns. However, there were no consistent trends in the phylodiversity patterns based on random taxon sampling compared to targeted sampling, or within individual clades compared to the complete dataset. Using pruned and reconstructed phylogenies resulted in similar patterns of phylodiversity, while chronograms in some cases led to significantly different results from phylograms. The methods commonly used in community phylogenetic studies can significantly impact the results, potentially influencing both inferences of community assembly and conservation decisions. We highlight the need for both careful selection of methods in community phylogenetic studies and appropriate interpretation of results, depending on the specific questions to be addressed. Measures of phylogenetic diversity are calculated based on the topology and branch lengths of phylogenetic trees. Using an empirical dataset of 14 communities in North Central Florida, we found that the taxon sampling strategy and the type of phylogeny used to calculate phylogenetic diversity can significantly influence the patterns of phylogenetic diversity that are observed. These different methodologies can result in different conclusions, so methods for community phylogenetic studies should be chosen with care.

Understory Community Assembly Following Wildfire in Boreal Forests: Shift From Stochasticity to Competitive Exclusion and Environmental Filtering

Article

Full-text available

Dec 2018

Understory vegetation accounts for the majority of plant species diversity and serves as a driver of overstory succession and nutrient cycling in boreal forest ecosystems. However, investigations of the underlying assembly processes of understory vegetation associated with stand development following a wildfire disturbance are rare, particularly in Eurasian boreal forests. In this study, we measured the phylogenetic and functional diversity and trait dispersions of understory communities and tested how these patterns changed with stand age in the Great Xing'an Mountains of Northeastern China. Contrary to our expectation, we found that understory functional traits were phylogenetically convergent. We found that random patterns of phylogenetic, functional, and trait dispersions were dominant for most of our surveyed plots, indicating that stochastic processes may play a crucial role in the determination of understory community assembly. Yet, there was an evidence that understory community assembly was also determined by competitive exclusion and environmental filtering to a certain degree, which was demonstrated by the observed clustered phylogenetic and functional patterns in some plots. Our results showed that phylogenetic diversity significantly decreased, while functional diversity increased with stand age. The observed shift trends in phylogenetic and functional patterns between random to clustering along with stand age, which suggested that understory community assembly shifted from stochasticity to competitive exclusion and environmental filtering. Our study presented a difference to community assembly and species coexistence theories insisted solely on deterministic processes. These findings indicated that Eurasian boreal understory communities may be primarily regulated by stochastic processes, providing complementary evidence that stochastic processes are crucial in the determination of community assembly both in tropical and boreal forests.

Metacommunity phylogenteic structure along environmental gradients

Preprint

Full-text available

Aug 2017

Diogo Borges Provete

Phylogenetic information has increasingly been included in studies of local communities and also at broad spatial scales. Despite recent criticisms in the last four years, phylogenetic relationships may still provide insights into theorganization and assembly of ecological communities. The objectives of this study were 1) to review the history of the use of phylogenetic information, as well as criticisms and perspectives of its use in community ecology; 2) understand how the size and shape of phylogenetic trees and the phylogenetic structure of metacomunidaes affect the amount of variation accounted for by a eigenvectorbasedmethod used to describe the phylogenetic composition of metacomunidaes (PCPS); 3) to test the effect of diversity of evolutionary history (MNTD and MPD) and species richness as predictors of three variables of freshwater ecosystemfunctioning (productivity, respiration, and decomposition); and finally 4) to test how environmental gradients, especially pond canopy cover, influence the phylogenetic structure of an anuran metacommunity from southeastern Brazil. Ifound that the structure of metacommunities had greater impact on eigenvalues of PCPS than tree shape metrics, such as symmetry and stemminess. In addition, decomposition and respiration were best predicted by MNTD as a linear function, while productivity was affected by the quadratic term of MNTD. Finally, pond canopy cover and floating vegetation strongly affected the phylogenetic structureof the anruan metacommunity, influencing lineage sorting. These findings 1) can help users interpret the results of PCPS; 2) provide better understand of the effectof species loss in multitrophic, freshwater ecosystems; and 3) improve our knowledge about the effect of canopy cover on the lineage composition in anuran metacomunities.

Article

Jan 2017

Species interactions in nature can be positive or negative. The stress gradient hypothesis (SGH) states that the strength of positive interactions increases with increasing stress. The phylogenetic limiting similarity hypothesis (PLSH) states that competition intensity is likely to be greater between closely related species than between distantly related species. Testing the SGH, the PLSH and determining the factors that influence species interactions with changing stress levels are important for ecosystem conservation and restoration. In the following study we conducted experiments to investigate the effects of salinity stress, phylogenetic relatedness (i.e., the sum of branch lengths separating species on a phylogenetic tree), and species ecological strategy on interspecific interactions using eleven species found with in a salt marsh located in the Yellow River Delta, China. We found most of the species interactions across increasing salinity levels to be inconsistent with the SGH. The net outcomes of interspecific interactions were significantly affected by multiple factors, including salinity stress, phylogenetic distance, ecological strategy, and the interaction between salinity and phylogenetic distance. Importantly, with increasing phylogenetic distance separating a pair species, the likelihood of facilitative interactions was increased and the likelihood of competitive interactions was reduced; this relationship was especially strong at medium and high salinities and supports the PLSH.

Algal polycultures enhance coproduct recycling from hydrothermal liquefaction

Article

Nov 2016

The aim of this study was to determine if polycultures of algae could enhance tolerance to aqueous-phase coproduct (ACP) from hydrothermal liquefaction (HTL) of algal biomass to produce biocrude. The growth of algal monocultures and polycultures was characterized across a range ACP concentrations and sources. All of the monocultures were either killed or inhibited by 2% ACP, but polycultures of the same species were viable at up to 10%. The addition of ACP increased the growth rate (up to 25%) and biomass production (53%) of polycultures, several of which were more productive in ACP than any monoculture was in the presence or absence of ACP. These results suggest that a cultivation process that applies biodiversity to nutrient recycling could produce more algae with less fertilizer consumption.

Functional dissimilarity, not phylogenetic relatedness, determines interspecific interactions among plants in the Tibetan alpine meadows

Article

Full-text available

Aug 2016

The hypotheses suggesting that the nature and strength of species interactions should be determined by phylogenetic relatedness have important implications for the understanding of community structure. However, to date, there is limited empirical evidence to support them. At least two basic conditions need to be met in order to expect species interactions to be determined by evolutionary relatedness: a phylogenetic signal in the traits involved in the interactions and changes in the interactions as species are more ecologically similar. Here, we report results of a removal experiment in the Chinese Tibetan plateau in which we directly assessed if the nature and/or strength of interactions among twelve alpine meadow plant species were influenced by their phylogenetic relatedness and/or their functional dissimilarity. For each plant species, we compared its biomass production when grown alone to its biomass in presence of another species and used it as a measure of species interactions. Competition between pairs of species was more frequent than facilitation, with 60% of interactions resulting in plants producing less biomass when a second species was present. We found no effect of phylogenetic relatedness on the prevalence or intensity of competition or facilitation, presumably as none of the studied traits showed phylogenetic signal. Functional dissimilarity based on maximum plant height alone was the best predictor of both the prevalence and strength of competition and facilitation, followed by functional dissimilarity using all five functional traits. Our results pinpoint the limited capacity of phylogenetic relatedness as predictor of species interactions; underlining the limitations of using phylogenetic dispersion patterns to infer mechanisms of community assembly. On the contrary, when the right functional traits are used, functional dissimilarity among species can predict both the nature and strength of their interactions; accentuating the relevance of trait-based approaches in community ecology research. This article is protected by copyright. All rights reserved.

Article

May 2016

Positive and negative interactions can occur simultaneously between plant species. According to the stress gradient hypothesis (SGH), species interactions shift towards more facilitative interactions or reductions in competition with increasing stress, whereas debate continues over whether evolutionary history influences the strength of species interactions. However, few studies have investigated the effects of phylogenetic relatedness (i.e., the sum of branch lengths separating species on a phylogeny) on the outcomes of interspecific interactions across stress levels. Therefore, we conducted a Bayesian meta-analysis on data collected from publications on plant interactions within coastal ecosystems in order to investigate the effects of phylogenetic relatedness on interspecific interactions across different stress levels. These analyses showed the effect sizes of species interactions on survival and growth to increase with stress increment, supporting the SGH in coastal ecosystems. However, phylogenetic relatedness did not lead to these differences of interspecific interactions between low and high stress. We found that species interactions affecting plant survival were not significantly influenced by phylogenetic relatedness; however, when evolutionary relationships of target and neighbor species were more phylogenetically distant, their interactions were more likely to facilitate growth of target species. Furthermore, the effect of the interaction between phylogenetic distance and stress on species interactions was negative. This suggests the observed net effects of phylogenetically distant neighbor species on target species were not due to true facilitation but reductions in competition when moving from low stress to high stress environments. According to these results, phylogenetic relatedness should be considered in choosing species for restoration of coastal ecosystem plant communities. Specifically, increasing the phylogenetic breadth of the assemblage is more likely to include species that have evolved to reduce stress on surrounding species through modification of the environment.

What Can Interaction Webs Tell Us About Species Roles?

Article

Full-text available

Jul 2015
PLOS COMPUT BIOL

The group model is a useful tool to understand broad-scale patterns of interaction in a network, but it has previously been limited in use to food webs, which contain only predator-prey interactions. Natural populations interact with each other in a variety of ways and, although most published ecological networks only include information about a single interaction type (e.g., feeding, pollination), ecologists are beginning to consider networks which combine multiple interaction types. Here we extend the group model to signed directed networks such as ecological interaction webs. As a specific application of this method, we examine the effects of including or excluding specific interaction types on our understanding of species roles in ecological networks. We consider all three currently available interaction webs, two of which are extended plant-mutualist networks with herbivores and parasitoids added, and one of which is an extended intertidal food web with interactions of all possible sign structures (+/+, -/0, etc.). Species in the extended food web grouped similarly with all interactions, only trophic links, and only nontrophic links. However, removing mutualism or herbivory had a much larger effect in the extended plant-pollinator webs. Species removal even affected groups that were not directly connected to those that were removed, as we found by excluding a small number of parasitoids. These results suggest that including additional species in the network provides far more information than additional interactions for this aspect of network structure. Our methods provide a useful framework for simplifying networks to their essential structure, allowing us to identify generalities in network structure and better understand the roles species play in their communities.

Eutrophication drives regime shift via changes in stoichiometric homeostasis-based submerged macrophyte assemblages

Article

Full-text available

May 2022

Homeostasis for phosphorus (HP) in submerged macrophytes may influence the susceptibility of lakes to regime shifts; however, the mechanisms linking submerged macrophyte HP to regime shifts remain unclear. We conducted an in situ mesocosm experiment to compare the dynamic responses of a high-HP species, Potamogeton maackianus, and a low-HP species, Hydrilla verticillata, to different phosphorus (P) level gradients, as well as their effects on phytoplankton inhibition. The biomass of P. maackianus under mesotrophic P (MP; P concentration 0.05 mg L−1) and eutrophic P (EP; P concentration 0.10 mg L−1) conditions was either non-significantly different from, or lower than that under oligotrophic P conditions (OP; P concentration under detection limit of 0.01 mg L−1). Conversely, H. verticillata biomass under EP was significantly higher than that under MP on day 90, whereas it died under OP. This variable response of submerged macrophyte species to P level gradients increased the relative growth advantage of H. verticillata compared to P. maackianus during eutrophication. The inhibition ratio of phytoplankton (IRP) for P. maackianus was ~15 times higher than that for H. verticillata under EP. Our study demonstrated a trend that submerged macrophyte assemblage IRP increased along with its assemblage HP. Thus, the changes in submerged macrophyte assemblages from high-HP species-dominance to low-HP species-dominance would erode its phytoplankton inhibition capacity, and further promote the regime shift from a clear-water state to a turbid state. Our results advance the regime shift theory from an ecological stoichiometry perspective and highlight the importance of high-HP submerged macrophyte species in the restoration of eutrophic lakes.

Relative abundance of invasive plants more effectively explains the response of wetland communities to different invasion degrees than phylogenetic evenness

Article

Full-text available

Jul 2021
J PLANT ECOL-UK

Aims Native plant communities are commonly invaded by invasive plants to different degrees. However, the relative contribution of the invasive plant abundance vs. phylogenetic evenness to the responses of wetland communities to different degrees of invasion is still unclear. In addition, whether such contribution varies with environmental conditions such as flooding is also unclear. Methods To address these questions, we chose Alternanthera philoxeroides as the invasive plant, and set up four invasive degrees by changing the community species composition under both flooding and non-flooding conditions. The relative abundance of A. philoxeroides and phylogenetic evenness changed simultaneously with the change in the community invasion degree. Important Findings The invasion degree significantly affected the individual biomass of A. philoxeroides and some native species. Variation partitioning showed that the relative abundance of A. philoxeroides contributed more to variation in community indicators than phylogenetic evenness, regardless of flooding. Spearman rank correlation test showed that the relative abundance of A. philoxeroides was negatively correlated with the individual biomass of A. philoxeroides and some native species, while the phylogenetic evenness was positively correlated with only a few native species. And their correlation strength and significance were all affected by specific species and flooded environment. In conclusion, our results suggest that the relative abundance of A. philoxeroides can more effectively explain the wetland community response to different invasion degrees than phylogenetic evenness, regardless of flooding.

Notes on coexistence of closely related Leiobunum rupestre and L. subalpinum (Opiliones, Eupnoi, Sclerosomatidae)

Article

Jun 2021

Two closely related, syntopic species, Leiobunum rupestre and L. subalpinum, spend the day at apparently randomly distributed resting sites. In this preliminary research, we studied differences in their microclimatic preferences at a locality in the Pohorje Mts., Slovenia. We measured air temperature and relative humidity at individual resting sites, and found that L. subalpinum occupied a slightly wider air temperature-relative humidity ecospace as compared to L. rupestre. Individuals of L. rupestre rested at more humid sites than L. subalpinum. Regression analyses revealed that the presence of L. rupestre was most likely at resting sites with air temperature in the range of 12–17°C and with relative air humidity of 98.1%. In contrast, the presence of L. subalpinum was most likely at resting sites with air temperature 23.1°C and relative air humidity in the range of 65–85%. Nevertheless, microclimatic niches of both species overlapped almost completely, indicating that niche filtering may allow the coexistence of the two species.

Ants climb plants because they cannot swim: ant presence on flowers during the flood season reduces the frequency of floral visitors

Article

Full-text available

Aug 2020

• Seasonal changes in environments may not only affect habitat connectivity but may also affect its use by species and their interactions. Thus, during the flood season, ants are forced to develop survival strategies such as vertical plant migration. • According to this, it has been hypothesized that the presence of ants may directly affect plant‐pollinator interactions. • Thus, we asked the following questions: (i) Are floral visitors of Hyptis brevipes expelled due to ant presence on inflorescences during the flood period? (ii) Is the ant effect mediated by the abundance of ants foraging on inflorescences? And, (iii) Does flower abundance predict the abundance of floral visits and ants? • We experimentally sampled 59 H. brevipes plants with and without ants during the flooded season, and observed no differences in flower abundance between ant treatments. • The probability of detaining floral visitors on H. brevipes increased with ant abundance and exceeded 50% possible repellency, but the probability of visitor deterrence was not related to flower abundance. Furthermore, the abundance of flowers did not predict the number of ants on H. brevipes individuals or the frequency of floral visits. • Consequently, ant repelling effects are pronounced when there are more ants foraging on plants. However, the ant repelling effect can be mitigated when plants flourish all year‐round and exhibit higher concentrations of flowers in the dry months. Additionally, the different sexual functions of plants may present specific responses due to the explosive pollination mechanism associated with ant effects.

Competition and specialization in an African forest carnivore community

Article

Full-text available

Aug 2019

Abstract Globally, human activities have led to the impoverishment of species assemblages and the disruption of ecosystem function. Determining whether this poses a threat to future ecosystem stability necessitates a thorough understanding of mechanisms underpinning community assembly and niche selection. Here, we tested for niche segregation within an African small carnivore community in Kibale National Park, Uganda. We used occupancy modeling based on systematic camera trap surveys and fine‐scale habitat measures, to identify opposing preferences between closely related species (cats, genets, and mongooses). We modeled diel activity patterns using kernel density functions and calculated the overlap of activity periods between related species. We also used co‐occupancy modeling and activity overlap analyses to test whether African golden cats Caracal aurata influenced the smaller carnivores along the spatial and/or temporal axes. There was some evidence that related species segregated habitat and activity patterns. Specialization was particularly strong among forest species. The cats and genets partitioned habitat, while the mongooses partitioned both habitat and activity period. We found little evidence for interference competition between African golden cats and other small carnivores, although weak interference competition was suggested by lower detection probabilities of some species at stations where African golden cats were present. This suggests that community assembly and coexistence in this ecosystem are primarily driven by more complex processes. The studied carnivore community contains several forest specialists, which are typically more prone to localized extinction. Preserving the observed community assemblage will therefore require the maintenance of a large variety of habitats, with a particular focus on those required by the more specialized carnivores.

A Network Perspective for Community Assembly

Article

Full-text available

Apr 2019

Species interactions are responsible for many key mechanisms that govern the dynamics of ecological communities. Variation in the way interactions are organized among species results in different network structures, which translates into a community's ability to resist collapse and change. To better understand the factors involved in dictating ongoing dynamics in a community at a given time, we must unravel how interactions affect the assembly process. Here, we build a novel, integrative conceptual model for understanding how ecological communities assemble that combines ecological networks and island biogeography theory, as well as the principles of niche theory. Through our conceptual model, we show how the rate of species turnover and gene flow within communities will influence the structure of ecological networks. We conduct a preliminary test of our predictions using plant-herbivore networks from differently-aged sites in the Hawaiian archipelago. Our approach will allow future modeling and empirical studies to develop a better understanding of the role of the assembly process in shaping patterns of biodiversity.

Larger Area Facilitates Richness-Function Effects in Experimental Microcosms

Article

Mar 2019

Species-area relationships (SAR) and biodiversity-ecosystem function (BEF) relationships are central patterns in community ecology. Although research on both patterns often invokes mechanisms of community assembly, both SARs and BEFs are generally treated as separate phenomena. Here we link the two by creating an experimental SAR in microcosm communities and show that greater species richness in larger areas is accompanied by greater ecosystem function. We then explore mechanisms of community assembly by determining whether rare, large, or high-biomass species are more likely to persist in the larger microcosms. Our results indicate that larger areas harbor more rare species of a wider range of body sizes and have higher functional diversity, implying that the addition of niche space that supports rare species underlies the effect of area on species richness and function. Our results suggest that the preservation of large areas is a potentially useful way of maximizing the provisioning of ecosystem services through the maintenance of biodiversity.

Relative performance of co-occurring alien plant invaders depends on traits related to competitive ability more than niche differences

Article

Full-text available

Apr 2019
BIOL INVASIONS

Christine S. Sheppard

Although conservation managers usually have to deal with multiple invaders that co-occur in native ecosystems, research to date has concentrated on the study of single highly invasive species. Consequently, this study aims to better understand the interactions among co-occurring alien plants. Specifically, I aim to determine how relative performance in mixture (compared to monoculture) depends on phylogenetic relatedness and similarity in functional traits. I investigated interactions among 18 alien annual plant species in Germany from six families in a multi-species common garden experiment, where plant individuals were grown in all pairwise species combinations. I measured growth, reproductive output and functional traits of the species, and determined phylogenetic and multivariate trait distances (representing niche differences) and individual trait hierarchies (representing average fitness differences that determine competitive superiority) between pairs. Across the 153 interspecific species combinations, individuals equally often experienced higher intraspecific or interspecific competition, with competitive responses varying greatly depending on species. Hierarchical differences in individual traits affected growth and seed production: being taller, having larger seed mass and higher specific leaf area benefitted relative performance of alien species when co-occurring with other aliens. Multivariate trait distance also had a positive effect on relative aboveground biomass production in mixture. Overall, hierarchical trait differences related to competitive ability appear to be more important than niche differences in determining performance for co-occurring alien plants. A better understanding on interaction type and strength among multiple plant invaders is crucial to determine appropriate management actions and contributes to ecological theory of community assembly.

Individual-based models of community assembly: Neighbourhood competition drives phylogenetic community structure

Article

Full-text available

Sep 2018

1.It is now commonplace for community ecologists to infer assembly processes from the evolutionary relatedness of co‐occurring species. Such inferences, however, have typically depended on assembly theories that assume competitive equilibrium and that are species‐based. In reality, all natural communities are dynamic, particularly during the course of succession, and the ecological interactions which drive phylogenetic community structure actually occur among neighboring individuals rather than species. 2.To bridge this gap between theory and reality, we examine how colonization, competition, and consequent replacement of individuals translate into phylogenetic community structure by using an individual‐based model. The model we use assumes a trade‐off between competition and colonization abilities and that the points where species fall on the trade‐off curve are phylogenetically conserved. 3.We find that the phylogenetic alpha diversity of a given community will be equal to or greater than the null expectation generated by randomly drawing individuals from communities at the same time step (i.e., phylogenetic overdispersion). This pattern results from the combination of interspecific differences in colonization ability and neighborhood competition that lead to individuals being regularly distributed in two‐dimensional space. 4.We also show that phylogenetic beta diversity increases with increasing temporal differences between two communities. However, when this positive relationship is analyzed only among the communities at close time steps, it becomes insignificant as they approach competitive equilibrium. We find similar patterns for functional alpha and beta diversity when phylogeny is replaced with functional traits. 5.Synthesis: Though questions concerning community assembly have often been spatially framed, our model shows that the span of the time frame can also affect, or even reverse, inferences about assembly processes. Our model also implies that a shift in the frame of reference from species to individuals brings a new perspective to community assembly. Careful consideration of non‐equilibrium and individual‐level aspects provides better insights into the consequences of the evolutionary and functional similarities of individuals on community assembly. This article is protected by copyright. All rights reserved.

Biodiversity improves the ecological design of sustainable biofuel systems

Article

Full-text available

Jun 2018

For algal biofuels to become a commercially viable and sustainable means of decreasing greenhouse gas emissions, growers are going to need to design feedstocks that achieve at least three characteristics simultaneously as follows: attain high yields; produce high quality biomass; and remain stable through time. These three qualities have proven difficult to achieve simultaneously under the ideal conditions of the laboratory, much less under field conditions (e.g., outdoor culture ponds) where feedstocks are exposed to highly variable conditions and the crop is vulnerable to invasive species, disease, and grazers. Here, we show that principles from ecology can be used to improve the design of feedstocks and to optimize their potential for “multifunctionality.” We performed a replicated experiment to test these predictions under outdoor conditions. Using 80 ponds of 1,100 L each, we tested the hypotheses that polycultures would outperform monocultures in terms of the following functions: biomass production, yield of biocrude from biomass, temporal stability, resisting population crashes, and resisting invasions by unwanted species. Overall, species richness improved stability, biocrude yield, and resistance to invasion. While this suggests that polycultures could outperform monocultures on average, invasion resistance was the only function where polycultures outperformed the best single species in the experiment. Due to tradeoffs among different functions that we measured, no species or polyculture was able to maximize all functions simultaneously. However, diversity did enhance the potential for multifunctionality—the most diverse polyculture performed more functions at higher levels than could any of the monocultures. These results are a key finding for ecological design of sustainable biofuel systems because they show that while a monoculture may be the optimal choice for maximizing short‐term biomass production, polycultures can offer a more stable crop of the desired species over longer periods of time. We tested the hypothesis that multi‐species polycultures of algae can be designed to improve performance in biofuel cultivation and outperform the best single species. Our experiment of 80 open ponds (1,100 L each) showed that polycultures can simultaneously improve crop stability, bio‐crude yield, and resistance to invasive algae ‐ three characteristics that have been difficult to attain under field conditions yet are essential for biofuels to become part of the renewable energy portfolio.

ele12932-sup-0001-supinfo

Data

Full-text available

Mar 2018

Supporting Information for Metabolic traits predict the effects of warming on phytoplankton competition Elvire Bestion, Bernardo García-Carreras, Charlotte-Elisa Schaum, Samraat Pawar,Gabriel Yvon-Durocher Ecology Letters, (2018), doi: 10.1111/ele.12932

Metabolic traits predict the effects of warming on phytoplankton competition

Article

Full-text available

Mar 2018

Understanding how changes in temperature affect interspecific competition is critical for predicting changes in ecological communities with global warming. Here, we develop a theoretical model that links interspecific differences in the temperature dependence of resource acquisition and growth to the outcome of pairwise competition in phytoplankton. We parameterised our model with these metabolic traits derived from six species of freshwater phytoplankton and tested its ability to predict the outcome of competition in all pairwise combinations of the species in a factorial experiment, manipulating temperature and nutrient availability. The model correctly predicted the outcome of competition in 72% of the pairwise experiments, with competitive advantage determined by difference in thermal sensitivity of growth rates of the two species. These results demonstrate that metabolic traits play a key role in determining how changes in temperature influence interspecific competition and lay the foundation for mechanistically predicting the effects of warming in complex, multi‐species communities.

Neighbour tolerance, not suppression, provides competitive advantage to non-native plants

Article

Full-text available

Mar 2018

High competitive ability has often been invoked as a key determinant of invasion success and ecological impacts of non-native plants. Yet our understanding of the strategies that non-natives use to gain competitive dominance remains limited. Particularly, it remains unknown whether the two non-mutually exclusive competitive strategies, neighbour suppression and neighbour tolerance, are equally important for the competitive advantage of non-native plants. Here, we analyse data from 192 peer-reviewed studies on pairwise plant competition within a Bayesian multilevel meta-analytic framework and show that non-native plants outperform their native counterparts due to high tolerance of competition, as opposed to strong suppressive ability. Competitive tolerance ability of non-native plants was driven by neighbour's origin and was expressed in response to a heterospecific native but not heterospecific non-native neighbour. In contrast to natives, non-native species were not more suppressed by hetero- vs. conspecific neighbours, which was partially due to higher intensity of intraspecific competition among non-natives. Heterogeneity in the data was primarily associated with methodological differences among studies and not with phylogenetic relatedness among species. Altogether, our synthesis demonstrates that non-native plants are competitively distinct from native plants and challenges the common notion that neighbour suppression is the primary strategy for plant invasion success.

Temporal variation in trophic relationships among three congeneric penguin species breeding in sympatry

Article

Full-text available

Mar 2018

Penguins are a monophyletic group in which many species are found breeding sympatrically, raising questions regarding how these species coexist successfully. Here, the isotopic niche of three sympatric pygoscelid penguin species was investigated at Powell Island, South Orkney Islands, during two breeding seasons (austral summers 2013–2014 and 2015–2016). Measurements of carbon (δ13C) and nitrogen (δ15N) stable isotope ratios were obtained from blood (adults) or feather (chicks) samples collected from Adélie Pygoscelis adeliae, chinstrap P. antarctica, and gentoo P. papua penguins. Isotopic niche regions (a proxy for the realized trophic niches) were computed to provide estimates of the trophic niche width of the studied species during the breeding season. The isotopic niche regions of adults of all three species were similar, but gentoo chicks had noticeably wider isotopic niches than the chicks of the other two species. Moderate to strong overlap in isotopic niche among species was found during each breeding season and for both age groups, suggesting that the potential for competition for shared food sources was similar during the two study years, although the actual level of competition could not be determined owing to the lack of data on resource abundance. Clear interannual shifts in isotopic niche were seen in all three species, though of lower amplitude for adult chinstrap penguins. These shifts were due to variation in carbon, but not nitrogen, isotopic ratios, which could indicate either a change in isotopic signature of their prey or a switch to an alternative food web. The main conclusions of this study are that (1) there is a partial overlap in the isotopic niches of these three congeneric species and that (2) they responded similarly to changes that likely occurred at the base of their food chain between the 2 years of the study.

Canopy cover and structural complexity affect the phylogenetic composition of a pond-dwelling Neotropical anuran metacommunity

Preprint

Full-text available

Jan 2018

Diogo Borges Provete

Phylogenetic information has been increasingly included into (meta)community assembly studies. However, recent studies have challenged the framework commonly used to infer processes from phylogenetic structure. Amphibians are good model organisms to study processes promoting structure in metacommunities, since they are subjected to different environmental and spatial processes throughout their biphasic life cycle. Pond canopy cover is one of these environmental factors that strongly influence the distribution of species and traits of several freshwater taxa, including larval amphibians (e.g., behavior, color, fin height, and length of intestine). Here, I tested the influence of pond canopy cover, floating vegetation, and pond morphology on the phylogenetic structure of an anuran metacommunity in the Atlantic Forest of Southeastern Brazil. I sampled tadpoles in 13 ponds and marshes from June 2008 and July 2009 in the Serra da Bocaina National Park, São Paulo. After building a metacommunity phylogeny, I used an eigenvector-based technique to describe the metacommunity phylogenetic composition (Principal Coordinates of Phylogenetic Structure, PCPS). I then run a db-RDA to evalute whether a subset of these eigenvectors can be explained by environmental variables. I found that pond canopy cover and floating vegetation were the main variables influencing lineage sorting in this metacommunity. Canopy cover separated hylid lineages from other families that were associated with open areas. Floating vegetation separated two hylid tribes (Cophomantini and Dendropsophini). Our results mainly suggest that the effect of canopy cover and floating vegetation on the structure of anuran metacommunity may affect not only species, but also entire lineages.

Ecological interactions and coexistence are predicted by gene expression similarity in freshwater green algae

Article

Apr 2017

1. Phenotypic variation controls the species interactions which determine whether or not species coexist. Long-standing hypotheses in ecology and evolution posit that phenotypic differentiation enables coexistence by increasing the size of niche differentiation. This hypothesis has only been tested using macroscopic traits to date, but niche differentiation, particularly of microscopic organisms , also occurs at the molecular and metabolic level. 2. We examined how phenotypic variation that arises at the level of gene expression over evolutionary time affects phytoplankton species interactions and coexistence. 3. We predicted that similarity in gene expression among species would decline with phylogenetic distance, and that reduced similarity in gene expression would weaken competition, increase facilitation and promote coexistence. 4. To test this, we grew eight species of freshwater green algae in monocultures and bicultures for 46 days in a laboratory microcosm experiment. We quantified the strength of species interactions by: (i) fitting Lotka–Volterra models to time-series densities and estimating interaction coefficients, and (ii) calculating relative densities that compare species' steady-state densities in biculture to those in monoculture. We used Illumina high throughput sequencing to quantify the expression of 1253 families of homologous genes, including a set of 17 candidate genes that we hypothesized a priori to be involved in competition or facilitation. 5. Synthesis. We found that closely related species had greater similarity in gene expression than did distantly related species, but as gene expression became more similar, species experienced weaker competition or greater facilitation, and were more likely to coexist. We identified gene functional categories that were uniquely differentially regulated in association with particular species interaction types. Contrary to common thinking in ecology and evolution, similarity in gene expression , and not differentiation, was associated with weaker competition, facilitation and coexistence.

Intraspecific and phylogenetic density-dependent seedling recruitment in a subtropical evergreen forest

Article

Full-text available

May 2017
OECOLOGIA

Recent evidence suggests that plant performance can be influenced by the phylogenetic diversity of neighboring plants. However, no study to date has examined the effect of such phylogenetic density dependence on the transition from seed to seedling. Using 6 years of data on seedling recruitment and seed rain of 13 species from 130 stations (one 0.5 m(2) seed trap and three adjacent 1 m(2) seedling plots) in a subtropical evergreen forest, we asked: (1) Does negative density dependence act across seed to seedling stages? (2) Is there evidence for phylogenetic density dependence during the seed to seedling transition? (3) Does the strength of density dependence vary among years? Generalized linear mixed-effects models were used to model seed to seedling transition as a function of conspecific seed and seedling densities, heterospecific seed and seedling densities, and mean phylogenetic distance of heterospecific seeds and seedling. Conspecific seed density had a significant negative effect on seedling transition rates for 12 of 13 focal species. In contrast, conspecific seedling density had a positive effect for 7 species, suggesting species-specific habitat preferences. Few species were significantly affected by the density or phylogenetic relatedness of heterospecific seeds and seedlings. Only conspecific seed density effects varied among years for most focal species. Overall, our results reveal that conspecific seed and seedling densities play a more important role than the density or relatedness of heterospecific seeds and seedlings during the seed to seedling stage, suggesting that species-specific seed predators, along with habitat preferences, may contribute to diversity maintenance in this forest.

Genome composition and phylogeny of microbes predict their co-occurrence in the environment

Article

Full-text available

Feb 2017
PLOS COMPUT BIOL

Olga K. Kamneva

The genomic information of microbes is a major determinant of their phenotypic properties, yet it is largely unknown to what extent ecological associations between different species can be explained by their genome composition. To bridge this gap, this study introduces two new genome-wide pairwise measures of microbe-microbe interaction. The first (genome content similarity index) quantifies similarity in genome composition between two microbes, while the second (microbe-microbe functional association index) summarizes the topology of a protein functional association network built for a given pair of microbes and quantifies the fraction of network edges crossing organismal boundaries. These new indices are then used to predict co-occurrence between reference genomes from two 16S-based ecological datasets, accounting for phylogenetic relatedness of the taxa. Phylogenetic relatedness was found to be a strong predictor of ecological associations between microbes which explains about 10% of variance in co-occurrence data, but genome composition was found to be a strong predictor as well, it explains up to 4% the variance in co-occurrence when all genomic-based indices are used in combination, even after accounting for evolutionary relationships between the species. On their own, the metrics proposed here explain a larger proportion of variance than previously reported more complex methods that rely on metabolic network comparisons. In summary, results of this study indicate that microbial genomes do indeed contain detectable signal of organismal ecology, and the methods described in the paper can be used to improve mechanistic understanding of microbe-microbe interactions.

Accounting for biotic interactions through alpha-diversity constraints in stacked species distribution models

Article

Full-text available

Dec 2016
Methods Ecol. Evol.

1. Species Distribution Models (SDM) are widely used to predict occupancy patterns at fine resolution over wide extents. However, SDMs generally ignore the effect of biotic interactions and tend to overpredict the number of species that can coexist at a given location and time (hereafter, the alpha-capacity). We developed an extension of SDMs that integrates species-level and community-level modelling to account for the above drivers. 2.The alpha-adjusted SDM takes the Probabilities of Occurrence (PoO) for all species of a community and the site’s alpha-capacity and adjusts the PoO, such that: a. their sum will equal the alpha-capacity as predicted by probability theory; and b. the adjusted PoO are dependent upon the relative suitability of each species for that site. The new method was tested using community data comprising 87 freshwater invertebrate species in an LTER watershed in Germany. We explored the ability of the method to predict alpha and beta-diversity patterns. We further focused on the effect on model performance at the species-level of the error associated with modelling alpha-capacity, of differences in gamma diversity (the size of the community) and of the type of community (random or guild-based). 3.The models that predicted alpha-capacity contained considerable error, and thus adjusting the PoO according to the modelled alpha-capacity resulted with decreased performance at the species level. However, when using the observed alpha-capacity to mimic a good alpha-capacity model, the alpha-adjusted SDMs usually resulted in increased performance. We further found that the alpha-adjusted SDM was better than the original SDM at predicting beta-diversity patterns, especially when using similarity indices that are sensitive to double absences. 4. Using the alpha-adjusted SDM approach may increase the predictive performance at the species and community levels if alpha-capacity can be assessed or modelled with sufficient accuracy, especially in relatively small communities of closely interacting species. With better models to predict alpha-capacity being developed, alpha-adjusted SDM has considerable potential to provide more realistic predictions of species-distribution patterns.

Manifold influences of phylogenetic structure on a plant–herbivore network

Article

Full-text available

Oct 2016
OIKOS

Ecologists are increasingly aware of the interplay between evolutionary history and ecological processes in shaping current species interaction patterns. The inclusion of phylogenetic relationships in studies of species interaction networks has shown that closely related species commonly interact with sets of similar species. Notably, the degree of phylogenetic conservatism in antagonistic ecological interactions is frequently stronger among species at lower trophic levels than among those at higher trophic levels. One hypothesis that accounts for this asymmetry is that competition among consumer species promotes resource partitioning and offsets the maintenance of dietary similarity by phylogenetic inertia. Here, we used a regional plant–herbivore network comprised of Asteraceae species and flower-head endophagous insects to evaluate how the strength of phylogenetic conservatism in species interactions differs between the two trophic levels. We also addressed whether the asymmetry in the strength of the phylogenetic signal between plants and animals depends on the overall degree of relatedness among the herbivores. We show that, beyond the previously reported compositional similarity, closely related species also share a greater proportion of counterpart phylogenetic history, both for resource and consumer species. Comparison of the patterns found in the entire network with those found in subnetworks composed of more phylogenetically restricted groups of herbivores provides evidence that resource partitioning occurs mostly at deeper phylogenetic levels, so that a positive phylogenetic signal in antagonist similarity is detectable even between closely related consumers in monophyletic subnetworks. The asymmetry in signal strength between trophic levels is most apparent in the way network modules reflect resource phylogeny, both for the entire network and for subnetworks. Taken together, these results suggest that evolutionary processes, such as phylogenetic conservatism and independent colonization history of the insect groups may be the main forces generating the phylogenetic structure observed in this particular plant–herbivore network system.

Community assembly and drivers of phytoplankton functional structure

Article

Full-text available

Oct 2016
FUNCT ECOL

1.We analysed the functional composition of coastal phytoplankton communities (n=7941) along the gradient from marine to brackish waters of the Baltic Sea, using species-specific morphological and ecological functional traits (ability to fix atmospheric nitrogen, mixotrophy, use of silica in cell walls, formation of chains or colonies, motility, accessory pigment composition, and size), to describe and measure the functional differences between species. 2.Mean pairwise functional distance of phytoplankton communities increased from spring to mid- and late summer in all regions, due to higher pigment diversity, increased share of mixotrophic and nitrogen fixing species, more diverse size distribution, and reduced dominance of silica users. 3.A null model that simulated the expected community composition from empirical spatial distribution and environmental preferences of individual taxa was used to partition the effects of habitat filtering and biotic interactions on the community assembly. 4.About every fourth community departed significantly from random expectations, signaling the notable effect of biotic interactions in the assembly of natural phytoplankton communities.

Towards Managing Food-Web Structure and Algal Crop Diversity in Industrial-Scale Algal Biomass Production

Article

Full-text available

Mar 2016

BACKGROUND: Consideration of ecological principles has brought new ideas that can be implemented to achieve sustainable production of algal biomass at the commercial-scale. In particular, the key ideas of top-down control of algal pests and the potential advantages of diversifying algal crops have encouraged researchers to explore food-web interactions in algal biomass cultivation platforms, and to investigate the characteristics of algal strains that could be used to assemble designed, multi-species consortia that outperform algal monocultures. OBJECTIVE/METHODS: To explore the practical applications of top-down control of algal pests and algal crop diversification, this paper reviews literature on agricultural and aquatic systems with consideration of the implementations of these ecological principles in managing commercial-scale algal cultivation. RESULTS: Our review suggests that careful management of food-web structure in algal cultivation platforms will be needed to maximize crop protection, and that temporal and spatial diversification of algal crops also may benefit industrial algal biofuels production. Extensive domestication and genetic improvements of algal strains are currently underway worldwide, and we suggest that careful selection of endogenous algal community which proliferates under selective environmental condition has the potential to engineer algal communities of high commercial interest. CONCLUSIONS: Overall, our review suggests that the careful management of food-web structure and algal crop diversity, as well as experiences and insights from modern agriculture can be used to guide the design and operation of industrial-scale algal biomass production systems. We urge thorough experimental tests of these ideas in both laboratory and field settings.

Phylogenetic impoverishment of plant communities following chronic human disturbances in the Brazilian Caatinga

Article

Full-text available

Jan 2016
ECOLOGY

Chronic disturbances, such as selective logging, firewood extraction and extensive grazing, may lead to the taxonomic and phylogenetic impoverishment of remaining old-growth forest communities worldwide; however, the empirical evidence on this topic is limited. We tested this hypothesis in the Caatinga vegetation – a seasonally dry tropical forest restricted to northeast Brazil. We sampled 11653 individuals (adults, saplings and seedlings) from 51 species in 29 plots distributed along a gradient of chronic disturbance. The gradient was assessed using a chronic disturbance index (CDI) based on five recognized indicators of chronic disturbances: proximity to urban center, houses and roads and the density of both people and livestock. We used linear models to test if mean effective number of lineages, mean phylogenetic distance and phylogenetic dispersion decreased with CDI and if such relationships differed among ontogenetic stages. As expected, the mean effective number of lineages and the mean phylogenetic distance were negatively related to CDI, and such diversity losses occurred irrespective of ontogeny. Yet the increase in phylogenetic clustering in more disturbed plots was only evident in seedlings and saplings, mostly because clades with more descendent taxa than expected by chance (e.g., Euphorbiaceae) thrived in more disturbed plots. This novel study indicates that chronic human disturbances are promoting the phylogenetic impoverishment of the irreplaceable woody flora of the Brazilian Caatinga forest. The highest impoverishment was observed in seedlings and saplings, indicating that if current chronic disturbances remain, they will result in increasingly poorer phylogenetically forests. This loss of evolutionary history will potentially limit the capacity of this ecosystem to respond to human disturbances (i.e., lower ecological resilience) and particularly their ability to adapt to rapid climatic changes in the region.

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

Article

Full-text available

Oct 2015

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.

Competitive avoidance not edaphic specialization drives vertical niche partitioning among sister species of ectomycorrhizal fungi

Article

Sep 2015
NEW PHYTOL

Soil depth partitioning is thought to promote the diversity of ectomycorrhizal (EM) fungal communities, but little is known about whether it is controlled by abiotic or biotic factors.In three bioassay experiments, we tested the role of vertical soil heterogeneity in determining the distributions and competitive outcomes of the EM sister species Rhizopogon vinicolor and Rhizopogon vesiculosus. We planted Pseudotsuga menziesii seedlings into soils that were either a homogenized mix of upper and lower depths or vertically stratified combinations mimicking natural field conditions.We found that both species colonized the upper or lower soil depths in the absence of competition, suggesting that their distributions were not limited by abiotic edaphic factors. In competition within homogeneous soils, R. vesiculosus completely excluded colonization by R. vinicolor, but R. vinicolor was able to persist when soils were stratified. The amount of colonization by R. vinicolor in the stratified soils was also significantly correlated with the number of multilocus genotypes present.Taken together, our findings suggest that the differential vertical distributions of R. vinicolor and R. vesiculosus in natural settings are probably attributable to competition rather than edaphic specialization, but that soil heterogeneity may play a key role in promoting EM fungal diversity.

Article

Full-text available

Jul 2022
CERNE

Background Factors determining the coexistence of species have been recognized since Darwin, but empirical studies have brought the relationship between niche similarity and competition into question. Knowing the mechanisms of coexistence makes it possible to predict biological invasions and determine better species combinations for the restoration and recovery of degraded areas. The aim of this study was to test the competition-relatedness hypothesis for semiarid tree species. Thus, an experiment was carried out with a phylogenetic gradient of tree species, planted in pairs. The phylogenetically closest pair consisted of congeneric species of the same clade, the intermediate pair comprised congeneric species of distinct clades, and the more distant pair were species of the same family. Results Our results show that the phylogenetically closest and the more distant pairs corroborated the competition-relatedness hypothesis, but the presence of one species with high competitive ability in the intermediate pair caused an unexpected pattern. Conclusion Niche differences are important for coexistence, but it is necessary to know the competitive ability of each species and the specific associations that are more productive to improve the efficiency of restoration programs and to reveal the degree of aggressiveness in the case of invasive species. Keywords: functional traits; facilitation; Cordia oncocalyx; Cordia glazioviana; Mimosa tenuiflora; Mimosa caesalpiniifolia; Libidibia férrea; Poincianella bracteosa

Uncovering the Drivers of Non-Native Plant Invasions Using Ecological Data Synthesis

Thesis

Full-text available

Jan 2019

Marina Golivets

Understanding what promotes invasiveness of species outside their native range and predicting which ecosystems and under which conditions will be invaded is an ultimate goal of the field of invasion ecology. Obtaining general answers to these questions requires synthesis of extensive yet heterogeneous empirical evidence, coupled with a solid theoretical background. In this dissertation, I sought to provide insight into the drivers of non-native plant invasions through combining and synthesizing ecological data from various sources using advanced statistical techniques. The results of this work are presented as three independent research studies. In the first study, I aimed to understand what determines competitive advantage of non-native over native plants: the ability to suppress other plants, tolerate them, or both. For this, I collected data from 192 studies on plant competition and analyzed them within a Bayesian multilevel meta-analytic framework. I showed that non-native plants outperform their native counterparts due to the high tolerance of competition, as opposed to strong suppressive ability. Competitive tolerance ability of non-native plants was driven by neighbor’s origin and was expressed in response to native species and not to other non-native species. This synthesis demonstrates that non-native plants are competitively distinct from native plants and challenges the common notion that neighbor suppression is the primary strategy for plant invasion success. In the second study, I quantified the extent to which regional, landscape and local environmental factors individually and jointly affect understory non-native invasive plants across northern US forests. I used boosted regression trees and Bayesian nonlinear regressions to analyze forest inventory data spanning 14 northern US states in combination with data on climate, land use, and disturbance. Regionally, the highest level of plant invasion was observed in hotter regions with lower annual precipitation and climate seasonality and higher summer precipitation. Locally, young forests with moist to wet soils and relatively flat topography in open, human-altered landscapes at low elevation were most susceptible to invasion. Climate and land use strongly interacted in their effect on plant invasions. This study refines the understanding of the non-native plant invasion process in northern US forests and the obtained models can be used to generate predictions under current and future environmental regimes to inform management. In the third study, I tested the relationship between the long-term history of recurrent canopy disturbance by a non-native invasive defoliator, the gypsy moth (Lymantria dispar), and the level of non-native plant invasion in northeastern US forests. I reconstructed 46 years (1970–2015) of gypsy-moth defoliation history and quantified the cumulative effect of defoliation on understory non-native invasive plant species using multivariate techniques and Bayesian nonlinear regressions. Contrary to what is commonly expected, the cumulative severity of gypsy moth defoliation tended to be negatively associated with the presence and richness of invasive plant species, although this association was weak. This study suggests that the effect of biotic disturbance on forest plant invasions may vary in both the magnitude and direction depending on characteristics of disturbance regime and its effect on resident biota, and this needs to be explicitly taken into account when predicting future plant invasions.

Microhabitats Shape Bacterial Community Composition, Ecosystem Function, and Genome Traits

Thesis

Jan 2018

Marian Schmidt

This dissertation helps to integrate bacteria into the broader field of ecology by investigating bacterial community composition and diversity as it relates to ecosystem function in microhabitats within freshwater systems of the Great Lakes Region. Here, I combine field- and laboratory-based measurements of observational data collected from three major types of lake ecosystems: inland lakes, a freshwater estuary (Muskegon Lake), and a Great Lake (Lake Michigan). First, to determine the primary controls on lake bacterial community composition, I assessed the influence of lake layer (i.e. stratification), lake productivity, and particle-association on the bacterial community across 11 inland lakes with varying productivity in Southwestern Michigan. I found that particle-association very strongly structures freshwater bacterial community composition. Second, I studied a freshwater estuarine lake, Muskegon Lake, which has a large spatio-temporal variation in bacterial heterotrophic productivity, to test whether there was an association between heterotrophic production and bacterial biodiversity (defined as the number of taxa and taxon abundance). I specifically focused on two co-occurring freshwater habitats that my first chapter showed to be populated by very distinct communities: particle-associated and free-living. Positive biodiversity-heterotrophic productivity relationships were found only in particles. Third, I performed a genome-based analysis of free-living specialists, particle-associated bacterial specialists, and generalists to characterize the genomic architecture and genetic traits that are associated with adaptations to these specific habitats. The genomes of particle-associated specialist bacteria were about twice the size of the genomes of free-living specialists and generalists, which had streamlined genomes. Fourth, to identify the bacterial taxa driving heterotrophic productivity across the large set of lake samples, I found that high nucleic acid (i.e., HNA) functional groups identified by flow cytometry can serve as a proxy for freshwater bacterial heterotrophic productivity, whereas low nucleic acid (i.e., LNA) functional groups cannot. Then, I used a machine learning approach to identify bacterial taxa associated with HNA and LNA. This allowed me to identify the bacterial taxa, which were often members of the Phylum Bacteroidetes, that are associated heterotrophic productivity. Finally, I investigated patterns of lake specificity and phylogenetic conservation of taxonomic groups. Throughout my dissertation, I found that there was very deep (Class to Phylum-level) phylogenetic conservation of which bacteria lived in which habitats, but not of what bacterial taxa contributed to HNA and LNA functional groups, and thus heterotrophic productivity. Positive biodiversity-heterotrophic productivity relationships only existed in particle-associated, and not free-living communities, and communities composed of more phylogenetically related organisms were more productive per-capita. These differences in biodiversity-ecosystem function relationships may in part be explained by particle-associated bacteria having larger genomes, higher nitrogen content, and more unique genes that provide the potential for niche complementarity. The taxa that drove HNA and LNA cell numbers, and by proxy heterotrophic productivity, were lake and time-specific and indicated that taxa could switch between the two functional groups. Overall, my dissertation elucidates the ecological and evolutionary effects of microhabitat structure on bacterial communities and genomes in natural systems.

Identity and provenance of neighbors, genotype-specific traits and abiotic stress affect intraspecific interactions in the annual legume Medicago truncatula

Preprint

Full-text available

Oct 2020

Accounting for intraspecific variation may improve our understanding of species coexistence. However, our knowledge of what factors maintain intraspecific variation is limited. We predicted that 1) a plant grows larger when with non-kin (i.e. different genotypes) than kin (i.e. same genotype) neighbors, 2) abiotic stress alters the outcome of kin vs. non-kin interactions, 3) genetic identity of plants affects composition of soil microbiome. We set up mini-communities of Medicago truncatula , where focal genotypes were grown together with two kin or two non-kin neighbors from different origins. We analyzed how origin, identity of interacting genotypes and abiotic stress affected growth and fruit production. We also analyzed the composition of soil microbial communities. Focal plants grew larger in non-kin than in kin mini-communities. This pattern was stronger in low level of abiotic stress and when interacting genotypes were from similar origins. However, genotypic variation in growth and response to competition had a stronger effect on growth than mini-community type. Plant genotype identity did not affect soil microbiome. We find that intraspecific variation is affected by genotype-specific traits and abiotic stress. Geographic, rather than genetic, distance among interacting genotypes affects the outcome of intraspecific interactions.

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

Article

Feb 2020
FEMS MICROBIOL ECOL

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. 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. Our work adds to the understanding of the highly distinct contributions to diversity and functioning contributed by bacteria in free-living and particle-associated habitats.

Metabolic traits predict the effects of warming on phytoplankton competition

Preprint

Full-text available

Dec 2017

Understanding how changes in temperature affect interspecific competition is critical for predicting changes in ecological communities as the climate warms. Here we develop a simple theoretical model that links interspecific differences in metabolic traits, which capture the temperature-dependence of resource acquisition, to the outcome of pairwise competition in phytoplankton. We parameterised our model with metabolic traits derived from six species of freshwater phytoplankton and tested its ability to predict the outcome of competition in all pairwise combinations of the species in a factorial experiment, manipulating temperature and nutrient availability. The model correctly predicted the outcome of competition in 71% of the pairwise experiments. These results demonstrate that metabolic traits play a key role in determining how changes in temperature influence interspecific competition and lay the foundation for developing theory to predict the effects of warming in complex, multi-species communities.

Ecological Stoichiometry Meets Ecological Engineering: Using Polycultures to Enhance the Multifunctionality of Algal Biocrude Systems

Article

Aug 2017
ENVIRON SCI TECHNOL

For algal biofuels to be economically sustainable and avoid exacerbating nutrient pollution, algal cultivation and processing must maximize rates of biofuel production while simultaneously minimizing the consumption of nitrogen (N) and phosphorus (P) fertilizers. We experimentally tested whether algal polycultures could be engineered to improve N- and P- nutrient-use efficiency compared to monocultures by balancing trade-offs in nutrient-use efficiency and biocrude production. We analyzed the flows of N and P through the processes of cultivation, biocrude production through hydrothermal liquefaction, and nutrient recycling in a laboratory-scale system. None of the six species we examined exhibited high N-efficiency, P-efficiency and biocrude production simultaneously; each had poor performance in at least one function (i.e. < 25th percentile). Polycultures of 2 to 6 species did not outperform the best species in any single function, but some polycultures exhibited more balanced performance and maintained all three functions at higher levels simultaneously than any of the monocultures (i.e. > 67th percentile). Moreover, certain polycultures came closer to optimizing all three functions than any of the monocultures. By balancing trade-offs between N- and P-efficiency and biocrude production, polycultures could be used to simultaneously reduce the demand for both N and P fertilizers by up to 85%.

Biotic Interactions Shape the Ecological Distributions of Staphylococcus Species

Article

Full-text available

Oct 2016

Importance: Decades of culture-based studies and more recent metagenomic studies have demonstrated that bacterial species in agriculture, medicine, industry, and nature are unevenly distributed across time and space. The ecological processes and molecular mechanisms that shape these distributions are not well understood because it is challenging to connect in situ patterns of diversity with mechanistic in vitro studies in the laboratory. Using tractable cheese rind biofilms and a focus on coagulase-negative staphylococcus (CNS) species, we demonstrate that fungi can mediate the ecological distributions of closely related bacterial species. One of the Staphylococcus species studied, S. saprophyticus, is a common cause of urinary tract infections. By identifying processes that control the abundance of undesirable CNS species, cheese producers will have more precise control on the safety and quality of their products. More generally, Staphylococcus species frequently co-occur with fungi in mammalian microbiomes, and similar bacterium-fungus interactions may structure bacterial diversity in these systems.

Evolutionary conservatism explains increasing relatedness of plant communities along a flooding gradient

Article

Sep 2016
NEW PHYTOL

Abiotic filters have been found either to increase or reduce evolutionary relatedness in plant communities, making it difficult to generalize responses of this major feature of biodiversity to future environmental change. Here, we hypothesized that the responses of phylogenetic structure to environmental change ultimately depend on how species have evolved traits for tolerating the resulting abiotic changes. Working within ephemeral wetlands, we tested whether species were increasingly related as flooding duration intensified. We also identified the mechanisms underlying increased relatedness by measuring root aerenchyma volume (RAV), a trait which promotes waterlogging tolerance. We found that species-specific responses to flooding explained most of the variation in occurrence for 63 vascular plant species across 5170 plots. For a subset of 22 species, we attributed these responses to variation in RAV. Large RAV specifically increased occurrence when flooding lasted for longer time periods, because large RAV reduced above-ground biomass loss. As large RAV was evolutionarily conserved within obligate wetland species, communities were more phylogenetically related as flooding increased. Our study shows how reconstructing the evolutionary history of traits that influence the responses of species to environmental change can help to predict future patterns in phylogenetic structure.

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

Article

Full-text available

Oct 2015

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 1,000-10,000 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.

The design, development and testing of a novel freshwater biomonitoring tool

Research

Full-text available

Jul 2015

Tom Gordon

Freshwater biomonitoring is often employed after an environmental disturbance, comparing invertebrate abundances at impacted sites to controls or references. However, the majority of biomonitoring practices ignore the now well-recognised concept that pollutions do not have to be lethal in order to compromise the function of an ecosystem. ‘Functional’ biomonitoring may provide a work-around by directly recording how an environment cycles its nutrients. I designed and built novel freshwater biomonitoring tools using the rate detritivores process leaf litter as a surrogate for ecosystem functioning. I tested the efficacy of these tools by comparing the rates of per-day leaf litter breakdown in the River Kennet at sites upstream and downstream of a recent pesticide spill. Upstream sites acted as a control whilst downstream sites were potentially suffering from impaired functioning. I also used several biomonitoring tools to investigate the effects of drought on per-day leaf litter breakdown in an experimental stream-mesocosm system. In both cases, I found evidence to suggest that per-day leaf litter breakdown was significantly slower in stressed environments when compared to controls. I found this to be in agreement with previous studies. I also compared leaf litter breakdown rates with invertebrate abundances taken at the same sites. Invertebrate abundance was not found to interact directly with breakdown rates, suggesting sub-lethal effects were at play. This design showed promise as a sensor of environmental stress. With further refinement, this biomonitoring tool may see employment at local, national and international scales and may become increasingly useful when considering more stringent freshwater legislation and the likelihood of damaging global environmental change.

Competition and Relative Yield: Estimation and Interpretation at Different Densities and Under Various Nutrient Concentrations Using Silybum Marianum and Cirsium Vulgare

Article

Full-text available

Mar 1988

(1) The role of the yield-density relationship in determining the choice of an additive or substitutive experimental design for competition experiments is examined, with particular reference to the design of multispecies experiments. A competition experiment between two thistle species Silybum marianum and Cirsium vulgaris at five density levels and six nutrient concentrations is described. (2) The design allows the influence of density and nutrient concentration on the relative yield in mixture compared with monoculture (RY) of the two species (as estimated from a substitutive design of N/2 plants in mixture) to be examined, and compared with that estimated from an additive design of N plants in mixture, where N is number of plants in monoculture. (3) Yields of the two species in monoculture show similar significant responses to both nutrient concentration and density: maximum yield occurs at a nutrient concentration four times standard Hoagland, and response to density is asymptotic. S. marianum has similar performance in mixture while C. vulgare yields are markedly reduced. Nutrient concentration has a significant influence on the RY of both species. A clear influence of density is only apparent at extremely high nutrient concentrations. (4) Acceptance of an asymptotic yield-density function implies that RY values between 0.5 and 1.0 cannot be interpreted unambiguously as being due to competition in substitutive experiments. Analysis of the substitutive design for S. marianum gives RY between 0.5 and 1.0, which cannot be interpreted as due to competition from C. vulgare. The additive design provides no evidence for such a competitive effect. RY values for C. vulgare are less than 0.5 in both designs indicating a competitive effect by S. marianum. (5) Choice of substitutive or additive design depends on knowledge of the yield-density function. Unequivocal results require a range of density combinations to be included in the design.

COMBO: A defined freshwater culture medium for algae and zooplankton

Article

Full-text available

Jul 1998
HYDROBIOLOGIA

In order to conduct experiments on interactions between animals and food organisms, it is necessary to develop a medium that adequately supports the growth of both algae and zooplankton without the need to alter the medium to accommodate either the algae or the animals. We devised a freshwater medium, named COMBO, that supports excellent growth of both algae and zooplankton. Two types of algae, Ankistrodesmus falcatus and Stephanodiscus hantzschii, were reared in COMBO and their growth rates were not significantly different from those of algae grown in a reference medium (WC). One of these algae, A. falcatus, was then fed to a cladoceran, Daphnia pulicaria, which was also cultured in COMBO, and the resulting fecundities of D. pulicaria were compared to those of animals reared in natural surface water. We also determined whether the value of COMBO as a medium for D. pulicaria was affected by modifications in nitrogen or phosphorus concentration to evaluate whether the new medium will be useful in nutritional research. Lowering the N or P content of COMBO did not affect the reproductive performance of D. pulicaria. Other researchers have also reported excellent growth and reproduction by numerous algae and zooplankton reared in COMBO. Our results suggest that COMBO is an effective artificial, defined culture medium capable of supporting robust growth and reproduction of both freshwater algae and zooplankton.

Theoretical Concepts and Empirical Approaches to Measuring Interaction Strength

Article

Full-text available

Mar 1998
ECOLOGY

Evaluating the strength of interactions among species is an important step in understanding the structure of natural communities and predicting how they will respond to changes in the biotic environment. Where feasible, accurate characterization of interaction strength can shift the theory of multispecies communities from identifying the vast range of possibilities to isolating the most likely possibilities. To derive generality in our un- derstanding of interaction strengths, however, they must be placed within a unified frame- work, a framework that can be applied to empirical situations. In this paper we first identify four different theoretical concepts of interaction strength prevalent in the literature (com- munity matrix, Jacobian matrix, inverse Jacobian, and removal matrix), showing how they are related to each other and how they are derived. We also demonstrate that their behavior is not necessarily concordant; hence it is important to identify clearly which concept of interaction strength is being discussed. Then we evaluate several observational and ex- perimental approaches to estimating interaction strength empirically, highlighting their ties to theory, if any, and the limitations and strengths of each approach. Finally, we apply several techniques to a simulated data set, based on an intertidal community, evaluating both accuracy and logistical ease of these approaches. We find that per capita interaction strength is often the most useful index to measure, that caution must be exercised in interpreting empirical estimates of interaction strength because of equilibrium assumptions and the potential confounding effect of indirect effects, and that concentrating on evaluating the relationship between empirically observed rates of change and species abundances may be a profitable way to proceed.

Trait-Based Community Ecology of Phytoplankton

Article

Full-text available

Dec 2008
ANNU REV ECOL EVOL S

Trait-based approaches are increasingly used in ecology. Phytoplankton communities, with a rich history as model systems in community ecology, are ideally suited for applying and further developing these concepts. Here we summarize the essential components of trait-based approaches and review their historical and potential application to illuminating phytoplankton community ecology. Major ecological axes relevant to phytoplankton include light and nutrient acquisition and use, natural enemy interactions, morphological variation, temperature sensitivity, and modes of reproduction. Trade-offs between these traits play key roles in determining community structure. Freshwater and marine environments may select for a different suite of traits owing to their different physical and chemical properties. We describe mathematical techniques for integrating traits into measures of growth and fitness and predicting how community structure varies along environmental gradients. Finally, we outline challenges and future...

Reducing redundancy in invasion ecology by integrating hypotheses into a single theoretical framework

Article

Full-text available

Jan 2009

Aim: invasion ecology includes many hypotheses. Empirical evidence suggests that most of these can explain the success of some invaders to some degree in some circumstances. If they all are correct, what does this tell us about invasion? We illustrate the major themes in invasion ecology, and provide an overarching framework that helps organize research and foster links among subfields of invasion ecology and ecology more generally. Location: global. Methods: we review and synthesize 29 leading hypotheses in plant invasion ecology. Structured around propagule pressure (P), abiotic characteristics (A) and biotic characteristics (B), with the additional influence of humans (H) on P, A and B (hereon PAB), we show how these hypotheses fit into one paradigm. P is based on the size and frequency of introductions, A incorporates ecosystem invasibility based on physical conditions, and B includes the characteristics of invading species (invasiveness), the recipient community and their interactions. Having justified the PAB framework, we propose a way in which invasion research could progress. Results: by highlighting the common ground among hypotheses, we show that invasion ecology is encumbered by theoretical redundancy that can be removed through integration. Using both holistic and incremental approaches, we show how the PAB framework can guide research and quantify the relative importance of different invasion mechanisms. Main conclusions: if the prime aim is to identify the main cause of invasion success, we contend that a top-down approach that focuses on PAB maximizes research efficiency. This approach identifies the most influential factors first, and subsequently narrows the number of potential causal mechanisms. By viewing invasion as a multifaceted process that can be partitioned into major drivers and broken down into a series of sequential steps, invasion theory can be rigorously tested, understanding improved and effective weed management techniques identified

Species phylogenetic relatedness, priority effects, and ecosystem functioning

Article

Full-text available

May 2012
ECOLOGY

Species immigration history can structure ecological communities through priority effects, which are often mediated by competition. As competition tends to be stronger between species with more similar niches, we hypothesize that species phylogenetic relatedness, under niche conservatism, may be a reasonable surrogate of niche similarity between species, and thus influence the strength of priority effects. We tested this hypothesis using a laboratory microcosm experiment in which we established bacterial species pools with different levels of phylogenetic relatedness and manipulated the immigration history of species from each pool into microcosms. Our results showed that strong priority effects, and hence multiple community states, only emerged for the species pool with the greatest phylogenetic relatedness. Community assembly also resulted in a significant positive relationship between bacterial phylogenetic diversity and ecosystem functions. Interestingly, these results emerged despite a lack of phylogenetic conservatism for most of the bacterial functional traits considered. Our results highlight the utility of phylogenetic information for understanding the structure and functioning of ecological communities, even when phylogenetically conserved functional traits are not identified or measured.

Is the originality of a species measurable? Ecol Lett

Article

Full-text available

Jun 2005
ECOL LETT

In this paper, we introduce the concept of ‘originality of a species within a set’ in order to indicate the average rarity of all the features belonging to this species. Using a phylogenetic tree of 70 species of New World terrestrial Carnivora, we suggest measuring the originality by a probability distribution. This maximizes the expected number of features shared by two species randomly drawn from the set. By using this new index, we take account of branch lengths whereas current indices of originality focus on tree topology. As a supplement to Nee and May's optimizing algorithm, we find that originality must be one of the criteria used in conservation planning.

Indices of plant competition

Article

Full-text available

Sep 2003
J ECOL

Summary 1 Mathematical indices, formed by combining several primary measures, can help researchers summarize, interpret and display results from plant competition experi- ments. This essay compiles and discusses more than 50 indices that have been used in studies of plant competition. 2 Indices allow researchers to quantify and express several attributes of plant com- petition, including competition intensity and importance, competitive effects and responses, and the outcome of competition. 3 Several qualities should be considered when selecting a competition index for use. These include specificity and clarity of meaning, mathematical and statistical pro- perties, density dependence, versatility and freedom from size bias. 4 Many indices are based on comparisons of plant performance in mixtures compared with pure stands or control plots. Additional measures of competition are also available from yield-density functions, size distributions and neighbourhood analysis. 5 Indices reflect the consequences of competition. In order to appreciate competitive processes, indices have to be used in conjunction with studies of the chronology, circum- stances and composition of plant associations.

Competitive interactions between forest trees are driven by species' trait hierarchy, not phylogenetic or functional similarity: Implications for forest community assembly

Article

Full-text available

May 2012
ECOL LETT

The relative importance of competition vs. environmental filtering in the assembly of communities is commonly inferred from their functional and phylogenetic structure, on the grounds that similar species compete most strongly for resources and are therefore less likely to coexist locally. This approach ignores the possibility that competitive effects can be determined by relative positions of species on a hierarchy of competitive ability. Using growth data, we estimated 275 interaction coefficients between tree species in the French mountains. We show that interaction strengths are mainly driven by trait hierarchy and not by functional or phylogenetic similarity. On the basis of this result, we thus propose that functional and phylogenetic convergence in local tree community might be due to competition-sorting species with different competitive abilities and not only environmental filtering as commonly assumed. We then show a functional and phylogenetic convergence of forest structure with increasing plot age, which supports this view.

Does phylogenetic relatedness influence the strength of competition among vascular plants? Perspect Plant Ecol

Article

Full-text available

Mar 2008
PERSPECT PLANT ECOL

A widely assumed but largely untested hypothesis central to ecology and evolutionary biology has been Charles Darwin's suggestion that closely related species will be more ecologically similar, and thus will compete more strongly with each other than they will with more distantly related species. We provide one of the first direct tests of the “competition-relatedness hypothesis” by combining two data sets: the relative competitive ability of 50 vascular plant species competing against 92 competitor species measured in five multi-species experiments, and measures of the phylogenetic relatedness of these species. In contrast to Darwin's assertion, there were weak relationships between the strength of competition and phylogenetic relatedness. Across all species studied, the competition-relatedness relationship was weak and not significant. This overall lack of pattern masked different responses of monocot and eudicot focal (phytometer) species. When monocots served as the focal (phytometer) species, the intensity of competition increased with the phylogenetic distance separating species, while competition decreased with phylogenetic distance for eudicot phytometers. These results were driven by the monocot-eudicot evolutionary split, such that monocots were poor competitors against eudicots, while eudicots are most strongly suppressed by other eudicots. There was no relationship between relatedness and competition for eudicots competing with other eudicots, while monocots did compete more intensely with closely related monocots than with distantly related monocots. Overall, the relationships between competition intensity and relatedness were weak compared to the strong and consistent relationships between competitive ability and functional traits such as plant size that have been reported by other studies. We suggest that Darwin's assertion that competition will be strongest among closely related species is not supported by empirical data, at least for the 142 vascular plant species in this study.

Article

Full-text available

Dec 2011
Proc Biol Sci

Biotic interactions assembling plant communities can be positive (facilitation) or negative (competition) and operate simultaneously. Facilitative interactions and posterior competition are among the mechanisms triggering succession, thus representing a good scenario for ecological restoration. As distantly related species tend to have different phenotypes, and therefore different ecological requirements, they can coexist, maximizing facilitation and minimizing competition. We suggest including phylogenetic relatedness together with phenotypic information as a predictor for the net effects of the balance between facilitation and competition in nurse-based restoration experiments. We quantify, by means of a Bayesian meta-analysis of nurse-based restoration experiments performed worldwide, the importance of phylogenetic relatedness and life-form disparity in the survival, growth and density of facilitated plants. We find that the more similar the life forms of neighbouring plants are the greater the positive effect of phylogenetic distance is on survival and density. This result suggests that other characteristics beyond life form are also contained in the phylogeny, and the larger the phylogenetic distance, the less is the niche overlap, and therefore the less is the competition. As a general rule, we can maximize the success of the nurse-based practices by increasing life-form disparity and phylogenetic distances between the neighbour and the facilitated plant.

Functional and phylogenetic diversity as predictors of biodiversity- Ecosystem-function relationships

Article

Full-text available

Aug 2011
ECOLOGY

How closely does variability in ecologically important traits reflect evolutionary divergence? The use of phylogenetic diversity (PD) to predict biodiversity effects on ecosystem functioning, and more generally the use of phylogenetic information in community ecology, depends in part on the answer to this question. However, comparisons of the predictive power of phylogenetic diversity and functional diversity (FD) have not been conducted across a range of experiments. To address how phylogenetic diversity and functional trait variation control biodiversity effects on biomass production, we summarized the results of 29 grassland plant experiments where both the phylogeny of plant species used in the experiments is well described and where extensive trait data are available. Functional trait variation was only partially related to phylogenetic distances between species, and the resulting FD values therefore correlate only partially with PD. Despite these differences, FD and PD predicted biodiversity effects across all experiments with similar strength, including in subsets that excluded plots with legumes and that focused on fertilization experiments. Two- and three-trait combinations of the five traits used here (leaf nitrogen percentage, height, specific root length, leaf mass per unit area, and nitrogen fixation) resulted in the FD values with the greatest predictive power. Both PD and FD can be valuable predictors of the effect of biodiversity on ecosystem functioning, which suggests that a focus on both community trait diversity and evolutionary history can improve understanding of the consequences of biodiversity loss.

Phylogenetically diverse grasslands are associated with pairwise interspecific processes that increase biomass

Article

Full-text available

Jul 2011
ECOLOGY

Biodiversity is an important determinant of primary productivity in experimental ecosystems. We combine two streams of research on understanding the effects of biodiversity on ecosystem function: quantifying phylogenetic diversity as a predictor of biodiversity effects in species-rich systems and the contribution of pairwise interspecific interactions to ecosystem function. We developed a statistical model that partitions the effect of biodiversity into effects due to community phylogenetic diversity and other community properties (e.g., average pairwise interaction, between- and within-functional-group effects, and so forth). The model provides phylogenetically based species-level explanations of differences in ecosystem response for communities with differing species composition. In two well-known grassland experiments, the model approach provides a parsimonious description of the effects of diversity as being due to the joint effect of the average pairwise statistical interaction and to community phylogenetic diversity. Effects associated with functional groupings of species in communities are largely explained by community phylogenetic diversity. The model approach quantifies a direct link between a measure of the evolutionary diversity of species and their interactive contribution to ecosystem function. It proves a useful tool in developing a mechanistic understanding of variation in ecosystem function.

Correction for Phylogenetic relatedness predicts priority effects in nectar yeast communities

Article

Full-text available

Jul 2011
Proc Biol Sci

Priority effects, in which the outcome of species interactions depends on the order of their arrival, are a key component of many models of community assembly. Yet, much remains unknown about how priority effects vary in strength among species in a community and what factors explain this variation. We experimented with a model natural community in laboratory microcosms that allowed us to quantify the strength of priority effects for most of the yeast species found in the floral nectar of a hummingbird-pollinated shrub at a biological preserve in northern California. We found that priority effects were widespread, with late-arriving species experiencing strong negative effects from early-arriving species. However, the magnitude of priority effects varied across species pairs. This variation was phylogenetically non-random, with priority effects stronger between closer relatives. Analysis of carbon and amino acid consumption profiles indicated that competition between closer relatives was more intense owing to higher ecological similarity, consistent with Darwin's naturalization hypothesis. These results suggest that phylogenetic relatedness between potential colonists may explain the strength of priority effects and, as a consequence, the degree to which community assembly is historically contingent.

Niche and fitness differences relate the maintenance of diversity to ecosystem function: Reply

Article

Full-text available

May 2011
ECOLOGY

The frequently observed positive correlation between species diversity and community biomass is thought to depend on both the degree of resource partitioning and on competitive dominance between consumers, two properties that are also central to theories of species coexistence. To make an explicit link between theory on the causes and consequences of biodiversity, we define in a precise way two kinds of differences among species: niche differences, which promote coexistence, and relative fitness differences, which promote competitive exclusion. In a classic model of exploitative competition, promoting coexistence by increasing niche differences typically, although not universally, increases the "relative yield total", a measure of diversity's effect on the biomass of competitors. In addition, however, we show that promoting coexistence by decreasing relative fitness differences also increases the relative yield total. Thus, two fundamentally different mechanisms of species coexistence both strengthen the influence of diversity on biomass yield. The model and our analysis also yield insight on the interpretation of experimental diversity manipulations. Specifically, the frequently reported "complementarity effect" appears to give a largely skewed estimate of resource partitioning. Likewise, the "selection effect" does not seem to isolate biomass changes attributable to species composition rather than species richness, as is commonly presumed. We conclude that past inferences about the cause of observed diversity-function relationships may be unreliable, and that new empirical estimates of niche and relative fitness differences are necessary to uncover the ecological mechanisms responsible for diversity-function relationships.

Burns JH, Strauss SY.. More closely related species are more ecologically similar in an experimental test. Proc Natl Acad Sci USA 108: 5302-5307

Article

Full-text available

Mar 2011
P NATL ACAD SCI USA

The relationship between phylogenetic distance and ecological similarity is key to understanding mechanisms of community assembly, a central goal of ecology. The field of community phylogenetics uses phylogenetic information to infer mechanisms of community assembly; we explore, the underlying relationship between phylogenetic similarity and the niche. We combined a field experiment using 32 native plant species with a molecular phylogeny and found that closely related plant species shared similar germination and early survival niches. Species also competed more with close relatives than with distant relatives in field soils; however, in potting soil this pattern reversed, and close relatives might even have more mutalistic relationships than distant relatives in these soils. Our results suggest that niche conservatism (habitat filtering) and species interactions (competition or facilitation) structure community composition, that phylogenetic relationships influence the strength of species' interactions, and that conserved aspects of plant niches include soil attributes.

Phylogenetic metrics of community similarity. Am Nat 176(5):E128-E142

Article

Full-text available

Nov 2010
AM NAT

We derive a new metric of community similarity that takes into account the phylogenetic relatedness among species. This metric, phylogenetic community dissimilarity (PCD), can be partitioned into two components, a nonphylogenetic component that reflects shared species between communities (analogous to Sørensen' s similarity metric) and a phylogenetic component that reflects the evolutionary relationships among nonshared species. Therefore, even if a species is not shared between two communities, it will increase the similarity of the two communities if it is phylogenetically related to species in the other community. We illustrate PCD with data on fish and aquatic macrophyte communities from 59 temperate lakes. Dissimilarity between fish communities associated with environmental differences between lakes often has a phylogenetic component, whereas this is not the case for macrophyte communities. With simulations, we then compare PCD with two other metrics of phylogenetic community similarity, II(ST) and UniFrac. Of the three metrics, PCD was best at identifying environmental drivers of community dissimilarity, showing lower variability and greater statistical power. Thus, PCD is a statistically powerful metric that separates the effects of environmental drivers on compositional versus phylogenetic components of community structure.

The Origin of Species

Book

Jan 1998

Charles Darwin

Population biology of plants. Academic press, london

Article

Jan 1977

J.L. Harper

Article

Jun 2012

On competition.Verslag van landbouwkundige onderzoekingen

Article

C.T. De Wit

On Competition

Article

Jan 1960

C.T. de Wit

A rapid Bootstrap algorithm for the RAxML Web Servers

Article

Jan 2008

Replacement or Additive Designs for Competition Studies?

Article

Dec 1991

R. W. Snaydon

(1) Replacement and additive designs are compared for their ability to provide valid and interpretable measures of (a) resource complementarity, i.e. relative yield total (RYT), (b) competitive ability, and (c) severity of competition in binary mixtures. (2) In replacement designs, the density of one component of the mixture is confounded with that of the other, so that competition between plants of one component is confounded with competition between plants of different components; the design is therefore statistically invalid. Because of this confounding, values of the relative yield total (RYT), competitive ability and severity of competition in replacement designs are affected by: (a) the density of each component to density in its pure-stand; (b) the pattern of response of each to density; and (c) the proportions of the components in mixtures; interpretation of these indices is therefore difficult or impossible. (3) By contrast, additive designs give valid and interpretable values of each of the indices of competition, regardless of density or proportions. Various misconceptions about additive designs are considered. (4) The value of binary factorial designs in competition studies is explored, and methods of analysing the resulting data are briefly considered.

Assembly Rules, Null Models, and Trait Dispersion: New Questions from Old Patterns

Article

Oct 1995

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

Abstract

No full-text available