Trait‐based tests of coexistence mechanisms

Recent functional trait studies have shown that trait differences may favour certain species (environmental filtering) while simultaneously preventing competitive exclusion (niche partitioning). However, phenomenological trait‐dispersion analyses do not identify the mechanisms that generate niche partitioning, preventing trait‐based prediction of future changes in biodiversity. We argue that such predictions require linking functional traits with recognised coexistence mechanisms involving spatial or temporal environmental heterogeneity, resource partitioning and natural enemies. We first demonstrate the limitations of phenomenological approaches using simulations, and then (1) propose trait‐based tests of coexistence, (2) generate hypotheses about which plant functional traits are likely to interact with particular mechanisms and (3) review the literature for evidence for these hypotheses. Theory and data suggest that all four classes of coexistence mechanisms could act on functional trait variation, but some mechanisms will be stronger and more widespread than others. The highest priority for future research is studies of interactions between environmental heterogeneity and trait variation that measure environmental variables at within‐community scales and quantify species' responses to the environment in the absence of competition. Evidence that similar trait‐based coexistence mechanisms operate in many ecosystems would simplify biodiversity forecasting and represent a rare victory for generality over contingency in community ecology.     

Trait‐based approach confirms the importance of propagule limitation and assembly rules in old‐field restoration

Community assembly theory is suggested as a guiding principle for ecological restoration to help understand the mechanisms that structure biological communities and identify where restoration interventions are needed. We studied three hypotheses related to propagule limitation, stress‐dominance, and limiting similarity concepts in community assembly in a restoration field experiment with a trait‐based null model approach. The experiment aimed to assist the recovery of sand grassland on former arable land in the Kiskunság, Pannonian biogeographic region, Europe. Treatments included initial seeding of five grassland species, carbon amendment, low‐intensity mowing, and combinations in 1 m by 1 m plots in three old fields from 2003 to 2008. The distribution of 10 individual plant traits was compared to the null model and the effect of time and treatments were tested with linear mixed effect models. Initial seeding had the most visible impact on species and trait composition confirming propagule limitation in grassland recovery. Reducing nutrient availability through carbon amendment strengthened trait convergence for length of flowering as expected based on the stress‐dominance hypothesis. Mowing changed trait divergence to convergence for plant height with a strengthening impact with time, supporting our hypothesis of increasing dominance of limiting similarity with time. Our results support the idea that community assembly is simultaneously influenced by propagule limitation and multiple trait‐based processes that act through different traits. The limited impact of manipulating environmental filtering and limiting similarity compared to seeding, however, supports the view that only targeting the dispersal and environmental filters in parallel would improve restoration outcome.     

Trait‐based ecology of terrestrial arthropods

In focusing on how organisms' generalizable functional properties (traits) interact mechanistically with environments across spatial scales and levels of biological organization, trait‐based approaches provide a powerful framework for attaining synthesis, generality and prediction. Trait‐based research has considerably improved understanding of the assembly, structure and functioning of plant communities. Further advances in ecology may be achieved by exploring the trait–environment relationships of non‐sessile, heterotrophic organisms such as terrestrial arthropods, which are geographically ubiquitous, ecologically diverse, and often important functional components of ecosystems. Trait‐based studies and trait databases have recently been compiled for groups such as ants, bees, beetles, butterflies, spiders and many others; however, the explicit justification, conceptual framework, and primary‐evidence base for the burgeoning field of ‘terrestrial arthropod trait‐based ecology’ have not been well established. Consequently, there is some confusion over the scope and relevance of this field, as well as a tendency for studies to overlook important assumptions of the trait‐based approach. Here we aim to provide a broad and accessible overview of the trait‐based ecology of terrestrial arthropods. We first define and illustrate foundational concepts in trait‐based ecology with respect to terrestrial arthropods, and justify the application of trait‐based approaches to the study of their ecology. Next, we review studies in community ecology where trait‐based approaches have been used to elucidate how assembly processes for terrestrial arthropod communities are influenced by niche filtering along environmental gradients (e.g. climatic, structural, and land‐use gradients) and by abiotic and biotic disturbances (e.g. fire, floods, and biological invasions). We also review studies in ecosystem ecology where trait‐based approaches have been used to investigate biodiversity–ecosystem function relationships: how the functional diversity of arthropod communities relates to a host of ecosystem functions and services that they mediate, such as decomposition, pollination and predation. We then suggest how future work can address fundamental assumptions and limitations by investigating trait functionality and the effects of intraspecific variation, assessing the potential for sampling methods to bias the traits and trait values observed, and enhancing the quality and consolidation of trait information in databases. A roadmap to guide observational trait‐based studies is also presented. Lastly, we highlight new areas where trait‐based studies on terrestrial arthropods are well positioned to advance ecological understanding and application. These include examining the roles of competitive, non‐competitive and (multi‐)trophic interactions in shaping coexistence, and macro‐scaling trait–environment relationships to explain and predict patterns in biodiversity and ecosystem functions across space and time. We hope this review will spur and guide future applications of the trait‐based framework to advance ecological insights from the most diverse eukaryotic organisms on Earth.     

Trait‐based community assembly of aquatic macrophytes along a water depth gradient in a freshwater lake

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Trait‐mediated community assembly: distinguishing the signatures of biotic and abiotic filters

Conflicting hypotheses predict how traits mediate species establishment and community assembly. Traits of newly establishing individuals are predicted to converge, or be more similar to the resident, preexisting community, when the biotic or abiotic environment favors a single best phenotype, but are predicted to diverge when trait differences reduce competitive interactions. We tested these competing hypotheses using transplant seedlings in an old‐field environment, and assessed the contribution of inter‐ and intra‐specific transplant trait variation to community‐level patterns. Using a soil moisture gradient and resident plant removals, we determined when traits of newly‐establishing plants converge or diverge from the resident community by calculating community weighted mean traits for transplant and resident communities. We saw evidence of environmentally‐ and competitively‐driven trait shifts that resulted in both trait convergence and divergence from the resident community, whose traits reflect the combined effects of both drivers. Leaf dry matter content (LDMC) of transplants diverged in the presence of competition, whereas plant height and stem‐specific density (SSD) showed the opposite pattern, converging with the resident community in their presence. Specific leaf area (SLA) shifted with competition but did not reflect resident community SLA. All transplant traits were influenced by soil moisture, often in an interaction with competition, indicating that the strength of convergence or divergence is contingent on the abiotic environment. Intraspecific differences in transplant traits among treatments were evident in three of four traits; intraspecific height and SLA trends mirrored transplant community‐level trends, whereas intraspecific shifts in SSD were distinct from community‐level trends. Our study shows competition between plant species may cause traits of newly establishing plants to converge with the resident community, as frequently as it selects for trait divergence. These opposing effects of competition suggest that it plays a pervasive role in both intraspecific and species‐level trait differences among communities.     

Trait‐divergence assembly rules have been demonstrated: Limiting similarity lives! A reply to Grime

The recent Forum contribution by Grime (2006) contrasts the MacArthur/Diamond assembly‐rule approach to studying plant communities with the study of environmental trait gradients. Both are valid and useful. In doing so, Grime declares that the assembly rules model, in which negative interactions between plants act with limiting similarity to cause local trait divergence, is “not supported by empirical study of plant communities”. This is, he says, the agony of community ecology. I show that there is now abundant evidence for assembly rules, and no agony.     

How two become one: HJURP dimerization drives CENP‐A assembly

EMBO J 32 15, 2113–2124 doi:10.1038/emboj.2013.142; published online June142013Curr Biol 23 9, 764–769 doi:10.1016/j.cub.2013.03.037; published online May062013Curr Biol 23 9, 770–774 doi:10.1016/j.cub.2013.03.042; published online May062013CENP-A containing nucleosomes epigenetically specify centromere position on chromosomes. Deposition of CENP-A into chromatin is mediated by HJURP, a specific CENP-A chaperone. Paradoxically, HJURP binding sterically prevents dimerization of CENP-A, which is critical to form functional centromeric nucleosomes. A recent publication in The EMBO Journal (Zasadzińska et al, 2013) demonstrates that HJURP itself dimerizes through a C-terminal repeat region, which is essential for centromeric assembly of nascent CENP-A.CENP-A containing nucleosomes have a well-established role in the epigenetic specification of centromere position. However, the composition of the CENP-A nucleosome has been the subject of intense investigation and debate (as has been extensively reviewed, e.g., in Black and Cleveland, 2011). X-ray crystallography data, biochemical interaction experiments and in vivo mutational analysis provide strong evidence that CENP-A nucleosomes are octameric (CENP-A/H4/H2A/H2B)₂, analogous to their histone H3-containing counterparts (Tachiwana et al, 2011; Bassett et al, 2012). Alternatively, based primarily on AFM data and nucleosome crosslinking assays, a tetrameric CENP-A/H4/H2A/H2B ‘hemisome'' has been proposed to be present at centromeres, at least during part of the cell cycle (Dalal et al, 2007; Bui et al, 2012). Whether both nucleosome types exist under specific conditions remains an unresolved question. However, recent studies by the Maddox and Black labs have reported single-molecule fluorescence measurements of CENP-A nucleosomes and high-resolution DNA protection assays of centromeric chromatin, respectively, both of which indicate that octamers are the predominant species of CENP-A in vivo (Hasson et al, 2013; Padeganeh et al, 2013).HJURP is the centromeric histone chaperone that is responsible for timely assembly of CENP-A nucleosomes. HJURP binds to soluble CENP-A and is recruited to centromeric chromatin in early G1 phase, concurrently with nascent CENP-A (Stellfox et al, 2013). Importantly, HJURP facilitates CENP-A nucleosome formation in vitro and its transient targeting to non-centromeric chromatin is sufficient to stably deposit CENP-A at these sites in vivo (Barnhart et al, 2011). Together, these observations identify HJURP as a bona fide centromeric CENP-A histone assembly factor.However, there is an apparent discrepancy between the role of HJURP in CENP-A assembly and the octameric nature of CENP-A nucleosomes. The crystal structure of the human prenucleosomal complex clearly shows that HJURP binds to CENP-A/H4 dimers in a manner that precludes CENP-A/H4 hetero-tetramerization (Hu et al, 2011). Interestingly, however, mutational analysis of CENP-A has shown that tetramerization is crucial for centromere assembly (Bassett et al, 2012). Thus, a mechanism must exist to allow for two trimeric HJURP/CENP-A/H4 complexes to coordinately assemble a tetrameric (CENP-A/H4)₂ particle.In this issue, a study by the Foltz lab sheds light on these paradoxical observations (Zasadzińska et al, 2013). Human HJURP contains two C-terminal repeat regions (HJURP C-terminal domains; HCTD). Expression of short fragments of HJURP containing either of these was sufficient to allow for centromere targeting. However, depletion of endogenous HJURP abolished centromere targeting of the C-terminally located HCTD2 fragment, without affecting the localization of the fragment containing HCTD1. These observations suggest that HCTD1 is required for centromere targeting, while HCTD2 allows for HJURP dimerization. Indeed, the authors go on to show that the latter fragment is both necessary and sufficient to form functional dimers of HJURP. RNAi replacement experiments show that HJURP lacking the HCTD2 dimerization domain is incapable of loading nascent CENP-A into centromeres. Importantly, Zasadzińska et al (2013) demonstrate that the defect in CENP-A loading can be directly attributed to a lack of HJURP dimerization. In an elegant experiment where the HCTD2 containing domain is replaced by an unrelated dimerization domain (that of bacterial LacI), CENP-A assembly is rescued to wild-type levels (Figure 1). This indicates that dimerization of HJURP is an essential step in centromeric chromatin assembly and provides a potential mechanism for the assembly of tetrameric (CENP-A/H4)₂ structures into chromatin as precursors to octameric nucleosomes.Open in a separate windowFigure 1Human HJURP contains separate protein domains that are responsible for CENP-A/H4 binding (blue), centromere targeting (brown) and dimerization (red). Full-length HJURP containing all these domains is capable of assembling CENP-A nucleosomes at centromeres (left). Zasadzińska et al (2013) now show that HJURP lacking the dimerization domain is still able to localize to centromeres, but is unable to assemble CENP-A nucleosomes (middle). However, replacement of the HJURP dimerization domain by an exogenous dimerization domain fully rescues the capability to form CENP-A nucleosomes at centromeres (right). These findings show that HJURP dimerization is an essential feature in the process of nucleosome formation, and explain how (CENP-A/H4)₂ tetramers can be formed by a chaperone that exclusively binds to CENP-A/H4 dimers.While the composition of the HJURP complex suggests a likely mechanism for the formation of octameric nucleosomes, this poses a new challenge to the field. Future studies will be needed to dissect how the shielded HJURP-bound state of CENP-A/H4 can transition to a tetramer on DNA. Interestingly, HJURP is not the only histone chaperone that exclusively binds to histone dimers. Crystal structures of trimeric complexes of both Asf1a/H3.1/H4 (English et al, 2006) as well as DAXX/H3.3/H4 (Elsässer et al, 2012) clearly show sterical incompatibility between chaperone binding and histone tetramerization. It follows that efficient chromatin assembly requires a mode for two histone chaperones to deposit histone dimers in a coordinated fashion, e.g., through dimerization as has been shown for Nap1 (McBryant and Peersen, 2004) and now for HJURP. However, dimerization does not appear to be a universal feature for histone chaperones, as a single CAF1 chaperone is able to bind two H3/H4 dimers as well as (H3/H4)₂ tetramers (Winkler et al, 2012). Thus, while deposition of H3.1/H4 at the replication fork may be driven by the high density of pre-assembly complexes, assembly of nucleosomes containing the replacement variant H3.3, H3.1 nucleosomes at DNA damage sites, and CENP-A at the centromere would require a more active form of coordination. Histone chaperone dimerization may therefore be a common feature in the pipeline to chromatin formation.In summary, Zasadzińska et al (2013) propose a solution to a paradox in the assembly pathway of CENP-A. They show that while each HJURP molecule can exclusively bind a single CENP-A/H4 dimer, HJURP itself dimerizes, ultimately allowing for the formation of tetrameric (CENP-A/H4)₂ structures in chromatin. Interestingly, exclusive dimer binding has been observed for a number of histone chaperones, suggesting that chaperone dimerization may be a more general process in the nucleosome assembly pathway.     

Plant–mycorrhizal fungus co‐occurrence network lacks substantial structure

The interactions between plants and arbuscular mycorrhizal fungi (AMF) maintain a crucial link between macroscopic organisms and the soil microbial world. These interactions are of extreme importance for the diversity of plant communities and ecosystem functioning. Despite this importance, only recently has the structure of plant–AMF interaction networks been studied. These recent studies, which used genetic data, suggest that these networks are highly structured, very similar to plant–animal mutualistic networks. However, the assembly process of plant–AMF communities is still largely unknown, and an important feature of plant–AMF interactions has not been incorporated: they occur at an extremely localized scale. Studying plant–AMF networks in a spatial context seems therefore a crucial step. This paper studies a plant–AMF spatial co‐occurrence network using novel methodology based on information theory and a unique set of spatially explicit species‐level data. We apply three null models of which only one accounts for spatial effects. We find that the data show substantial departures from null expectations for the two non‐spatial null models. However, for the null model considering spatial effects, there are few significant co‐occurrences compared with the other two null models. Thus, plant–AMF spatial co‐occurrences seem to be mostly explained by stochasticity, with a small role for other factors related to plant–AMF specialization. Furthermore, we find that the network is not significantly nested or modular. We conclude that this plant–AMF spatial co‐occurrence network lacks substantial structure and, therefore, plants and AMF species do not track each other over space. Thus, random encounters seem more important in the first step of the assembly of plant–AMF communities. Synthesis The symbiotic interaction between plants and arbuscular mycorrhizal fungi (AMF) is crucial for ecosystem functioning. However, the factors affecting the assembly of plant‐AMF communities are poorly understood. An important factor of the assembly of plant‐AMF communities has been overlooked: plant‐AMF interactions occur at a localized spatial scale. Our study investigated the importance of space in the structure of plant‐AMF communities. We studied a plant‐AMF spatial co‐occurrence network using a unique set of spatially explicit data and applied three null models. We found that plant‐AMF spatial co‐occurrences seem to be mostly explained by stochasticity. In particular, our study shows that this plant‐AMF spatial co‐occurrence network lacks substantial structure and, therefore, plants and AMF species do not track each other over space. Thus, random encounters seem to drive the assembly of plant‐AMF communities.     

Fine‐scale spatial ecology drives kin selection relatedness among cooperating amoebae

Cooperation among microbes is important for traits as diverse as antibiotic resistance, pathogen virulence, and sporulation. The evolutionary stability of cooperation against “cheater” mutants depends critically on the extent to which microbes interact with genetically similar individuals. The causes of this genetic social structure in natural microbial systems, however, are unknown. Here, we show that social structure among cooperative Dictyostelium amoebae is driven by the population ecology of colonization, growth, and dispersal acting at spatial scales as small as fruiting bodies themselves. Despite the fact that amoebae disperse while grazing, all it takes to create substantial genetic clonality within multicellular fruiting bodies is a few millimeters distance between the cells colonizing a feeding site. Even adjacent fruiting bodies can consist of different genotypes. Soil populations of amoebae are sparse and patchily distributed at millimeter scales. The fine‐scale spatial structure of cells and genotypes can thus account for the otherwise unexplained high genetic uniformity of spores in fruiting bodies from natural substrates. These results show how a full understanding of microbial cooperation requires understanding ecology and social structure at the small spatial scales microbes themselves experience.     

Climate drives among‐year variation in natural selection on flowering time

To predict long‐term responses to climate change, we need to understand how changes in temperature and precipitation elicit both immediate phenotypic responses and changes in natural selection. We used 22 years of data for the perennial herb Lathyrus vernus to examine how climate influences flowering phenology and phenotypic selection on phenology. Plants flowered earlier in springs with higher temperatures and higher precipitation. Early flowering was associated with a higher fitness in nearly all years, but selection for early flowering was significantly stronger in springs with higher temperatures and lower precipitation. Climate influenced selection through trait distributions, mean fitness and trait?fitness relationships, the latter accounting for most of the among‐year variation in selection. Our results show that climate both induces phenotypic responses and alters natural selection, and that the change in the optimal phenotype might be either weaker, as for spring temperature, or stronger, as for precipitation, than the optimal response.     

Trait‐mediated effects of predation across life‐history stages in container mosquitoes

1. It was determined if the predatory midge Corethrella appendiculata Grabham imposes a fitness cost in a native mosquito, Ochlerotatus triseriatus Say, and an invasive mosquito, Aedes albopictus Skuse. The hypothesis that decreased activity of immature prey in the presence of predator cues is associated with life history costs through all life cycle stages was tested. 2. In experiment 1, individual larvae of O. triseriatus or A. albopictus were raised in the presence or absence of predation cues at two resource levels. Prey were video recorded to detect behavioural responses and to measure development time, size at emergence, and adult longevity. In experiment 2, prey populations were reared in similar environments and the frequency of predator cue additions was varied. 3. Only O. triseriatus reduced its activity in the presence of predation cues. Predation cues were associated with longer immature development times and shorter adult life spans in O. triseriatus, whereas in A. albopictus, the cues were associated with a larger size of emerging adults. 4. In the present study, it was found that behavioural modifications during the larval stage can affect mosquitoes through multiple stages of their complex life cycle. The species‐specific behavioural differences are probably attributable to the longer evolutionary history O. triseriatus has with predators, relative to the invasive A. albopictus.     

Competitor avoidance drives within‐host feeding site selection in a passively dispersed herbivore

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